{"id":43633,"date":"2025-04-23T10:54:10","date_gmt":"2025-04-23T10:54:10","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/43633\/"},"modified":"2025-04-23T10:54:10","modified_gmt":"2025-04-23T10:54:10","slug":"pan-genomic-analysis-highlights-genes-associated-with-agronomic-traits-and-enhances-genomics-assisted-breeding-in-alfalfa","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/43633\/","title":{"rendered":"Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa"},"content":{"rendered":"<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"1.\">\n<p class=\"c-article-references__text\" id=\"ref-CR1\">Annicchiarico, P., Barrett, B., Brummer, E. C., Julier, B. &amp; Marshall, A. H. Achievements and challenges in improving temperate perennial forage legumes. Crit. Rev. Plant Sci. <b>34<\/b>, 327\u2013380 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1080\/07352689.2014.898462\" data-track-item_id=\"10.1080\/07352689.2014.898462\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1080%2F07352689.2014.898462\" aria-label=\"Article reference 1\" data-doi=\"10.1080\/07352689.2014.898462\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXhvVOnsbbK\" aria-label=\"CAS reference 1\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 1\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Achievements%20and%20challenges%20in%20improving%20temperate%20perennial%20forage%20legumes&amp;journal=Crit.%20Rev.%20Plant%20Sci.&amp;doi=10.1080%2F07352689.2014.898462&amp;volume=34&amp;pages=327-380&amp;publication_year=2015&amp;author=Annicchiarico%2CP&amp;author=Barrett%2CB&amp;author=Brummer%2CEC&amp;author=Julier%2CB&amp;author=Marshall%2CAH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"2.\">\n<p class=\"c-article-references__text\" id=\"ref-CR2\">Shen, C. et al. The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for alfalfa research. Mol. Plant <b>13<\/b>, 1250\u20131261 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.molp.2020.07.003\" data-track-item_id=\"10.1016\/j.molp.2020.07.003\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.molp.2020.07.003\" aria-label=\"Article reference 2\" data-doi=\"10.1016\/j.molp.2020.07.003\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhs1GrtLrI\" aria-label=\"CAS reference 2\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32673760\" aria-label=\"PubMed reference 2\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 2\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20chromosome-level%20genome%20sequence%20of%20the%20autotetraploid%20alfalfa%20and%20resequencing%20of%20core%20germplasms%20provide%20genomic%20resources%20for%20alfalfa%20research&amp;journal=Mol.%20Plant&amp;doi=10.1016%2Fj.molp.2020.07.003&amp;volume=13&amp;pages=1250-1261&amp;publication_year=2020&amp;author=Shen%2CC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"3.\">\n<p class=\"c-article-references__text\" id=\"ref-CR3\">Li, X. &amp; Brummer, E. C. Applied genetics and genomics in alfalfa breeding. Agronomy <b>2<\/b>, 40\u201361 (2012).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.3390\/agronomy2010040\" data-track-item_id=\"10.3390\/agronomy2010040\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.3390%2Fagronomy2010040\" aria-label=\"Article reference 3\" data-doi=\"10.3390\/agronomy2010040\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38XhsVSjtb%2FP\" aria-label=\"CAS reference 3\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 3\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Applied%20genetics%20and%20genomics%20in%20alfalfa%20breeding&amp;journal=Agronomy&amp;doi=10.3390%2Fagronomy2010040&amp;volume=2&amp;pages=40-61&amp;publication_year=2012&amp;author=Li%2CX&amp;author=Brummer%2CEC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"4.\">\n<p class=\"c-article-references__text\" id=\"ref-CR4\">Chen, H. et al. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nat. Commun. <b>11<\/b>, 2494 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41467-020-16338-x\" data-track-item_id=\"10.1038\/s41467-020-16338-x\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41467-020-16338-x\" aria-label=\"Article reference 4\" data-doi=\"10.1038\/s41467-020-16338-x\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXpvF2lt7w%3D\" aria-label=\"CAS reference 4\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32427850\" aria-label=\"PubMed reference 4\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7237683\" aria-label=\"PubMed Central reference 4\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 4\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Allele-aware%20chromosome-level%20genome%20assembly%20and%20efficient%20transgene-free%20genome%20editing%20for%20the%20autotetraploid%20cultivated%20alfalfa&amp;journal=Nat.%20Commun.&amp;doi=10.1038%2Fs41467-020-16338-x&amp;volume=11&amp;publication_year=2020&amp;author=Chen%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"5.\">\n<p class=\"c-article-references__text\" id=\"ref-CR5\">Long, R. et al. Genome assembly of alfalfa cultivar Zhongmu-4 and identification of SNPs associated with agronomic traits. Genomics Proteomics Bioinformatics <b>20<\/b>, 14\u201328 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.gpb.2022.01.002\" data-track-item_id=\"10.1016\/j.gpb.2022.01.002\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.gpb.2022.01.002\" aria-label=\"Article reference 5\" data-doi=\"10.1016\/j.gpb.2022.01.002\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXhvFKrsLvM\" aria-label=\"CAS reference 5\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=35033678\" aria-label=\"PubMed reference 5\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9510860\" aria-label=\"PubMed Central reference 5\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 5\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Genome%20assembly%20of%20alfalfa%20cultivar%20Zhongmu-4%20and%20identification%20of%20SNPs%20associated%20with%20agronomic%20traits&amp;journal=Genomics%20Proteomics%20Bioinformatics&amp;doi=10.1016%2Fj.gpb.2022.01.002&amp;volume=20&amp;pages=14-28&amp;publication_year=2022&amp;author=Long%2CR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"6.\">\n<p class=\"c-article-references__text\" id=\"ref-CR6\">Jayakodi, M., Schreiber, M., Stein, N. &amp; Mascher, M. Building pan-genome infrastructures for crop plants and their use in association genetics. DNA Res. <b>28<\/b>, dsaa030 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/dnares\/dsaa030\" data-track-item_id=\"10.1093\/dnares\/dsaa030\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fdnares%2Fdsaa030\" aria-label=\"Article reference 6\" data-doi=\"10.1093\/dnares\/dsaa030\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33484244\" aria-label=\"PubMed reference 6\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7934568\" aria-label=\"PubMed Central reference 6\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 6\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Building%20pan-genome%20infrastructures%20for%20crop%20plants%20and%20their%20use%20in%20association%20genetics&amp;journal=DNA%20Res.&amp;doi=10.1093%2Fdnares%2Fdsaa030&amp;volume=28&amp;publication_year=2021&amp;author=Jayakodi%2CM&amp;author=Schreiber%2CM&amp;author=Stein%2CN&amp;author=Mascher%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"7.\">\n<p class=\"c-article-references__text\" id=\"ref-CR7\">Pang, A. W. et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. <b>11<\/b>, R52 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/gb-2010-11-5-r52\" data-track-item_id=\"10.1186\/gb-2010-11-5-r52\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/gb-2010-11-5-r52\" aria-label=\"Article reference 7\" data-doi=\"10.1186\/gb-2010-11-5-r52\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20482838\" aria-label=\"PubMed reference 7\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2898065\" aria-label=\"PubMed Central reference 7\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 7\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Towards%20a%20comprehensive%20structural%20variation%20map%20of%20an%20individual%20human%20genome&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fgb-2010-11-5-r52&amp;volume=11&amp;publication_year=2010&amp;author=Pang%2CAW\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"8.\">\n<p class=\"c-article-references__text\" id=\"ref-CR8\">Zhang, Z. et al. Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. Plant Cell <b>27<\/b>, 1595\u20131604 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1105\/tpc.114.135848\" data-track-item_id=\"10.1105\/tpc.114.135848\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1105%2Ftpc.114.135848\" aria-label=\"Article reference 8\" data-doi=\"10.1105\/tpc.114.135848\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2MXhtFynt7zP\" aria-label=\"CAS reference 8\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=26002866\" aria-label=\"PubMed reference 8\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4498199\" aria-label=\"PubMed Central reference 8\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 8\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Genome-wide%20mapping%20of%20structural%20variations%20reveals%20a%20copy%20number%20variant%20that%20determines%20reproductive%20morphology%20in%20cucumber&amp;journal=Plant%20Cell&amp;doi=10.1105%2Ftpc.114.135848&amp;volume=27&amp;pages=1595-1604&amp;publication_year=2015&amp;author=Zhang%2CZ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"9.\">\n<p class=\"c-article-references__text\" id=\"ref-CR9\">Zhou, Y. et al. The population genetics of structural variants in grapevine domestication. Nat. Plants <b>5<\/b>, 965\u2013979 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41477-019-0507-8\" data-track-item_id=\"10.1038\/s41477-019-0507-8\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41477-019-0507-8\" aria-label=\"Article reference 9\" data-doi=\"10.1038\/s41477-019-0507-8\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31506640\" aria-label=\"PubMed reference 9\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 9\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20population%20genetics%20of%20structural%20variants%20in%20grapevine%20domestication&amp;journal=Nat.%20Plants&amp;doi=10.1038%2Fs41477-019-0507-8&amp;volume=5&amp;pages=965-979&amp;publication_year=2019&amp;author=Zhou%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"10.\">\n<p class=\"c-article-references__text\" id=\"ref-CR10\">Saxena, R. K., Edwards, D. &amp; Varshney, R. K. Structural variations in plant genomes. Brief. Funct. Genomics <b>13<\/b>, 296\u2013307 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bfgp\/elu016\" data-track-item_id=\"10.1093\/bfgp\/elu016\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbfgp%2Felu016\" aria-label=\"Article reference 10\" data-doi=\"10.1093\/bfgp\/elu016\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24907366\" aria-label=\"PubMed reference 10\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4110416\" aria-label=\"PubMed Central reference 10\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 10\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Structural%20variations%20in%20plant%20genomes&amp;journal=Brief.%20Funct.%20Genomics&amp;doi=10.1093%2Fbfgp%2Felu016&amp;volume=13&amp;pages=296-307&amp;publication_year=2014&amp;author=Saxena%2CRK&amp;author=Edwards%2CD&amp;author=Varshney%2CRK\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"11.\">\n<p class=\"c-article-references__text\" id=\"ref-CR11\">Gabur, I., Chawla, H. S., Snowdon, R. J. &amp; Parkin, I. A. Connecting genome structural variation with complex traits in crop plants. Theor. Appl. Genet. <b>132<\/b>, 733\u2013750 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1007\/s00122-018-3233-0\" data-track-item_id=\"10.1007\/s00122-018-3233-0\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/s00122-018-3233-0\" aria-label=\"Article reference 11\" data-doi=\"10.1007\/s00122-018-3233-0\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30448864\" aria-label=\"PubMed reference 11\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 11\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Connecting%20genome%20structural%20variation%20with%20complex%20traits%20in%20crop%20plants&amp;journal=Theor.%20Appl.%20Genet.&amp;doi=10.1007%2Fs00122-018-3233-0&amp;volume=132&amp;pages=733-750&amp;publication_year=2019&amp;author=Gabur%2CI&amp;author=Chawla%2CHS&amp;author=Snowdon%2CRJ&amp;author=Parkin%2CIA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"12.\">\n<p class=\"c-article-references__text\" id=\"ref-CR12\">Chen, S. et al. Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis. Nat. Plants <b>9<\/b>, 1986\u20131999 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41477-023-01565-z\" data-track-item_id=\"10.1038\/s41477-023-01565-z\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41477-023-01565-z\" aria-label=\"Article reference 12\" data-doi=\"10.1038\/s41477-023-01565-z\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXisFGit77I\" aria-label=\"CAS reference 12\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=38012346\" aria-label=\"PubMed reference 12\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 12\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Gene%20mining%20and%20genomics-assisted%20breeding%20empowered%20by%20the%20pangenome%20of%20tea%20plant%20Camellia%20sinensis&amp;journal=Nat.%20Plants&amp;doi=10.1038%2Fs41477-023-01565-z&amp;volume=9&amp;pages=1986-1999&amp;publication_year=2023&amp;author=Chen%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"13.\">\n<p class=\"c-article-references__text\" id=\"ref-CR13\">Gaut, B. S., Seymour, D. K., Liu, Q. &amp; Zhou, Y. Demography and its effects on genomic variation in crop domestication. Nat. Plants <b>4<\/b>, 512\u2013520 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41477-018-0210-1\" data-track-item_id=\"10.1038\/s41477-018-0210-1\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41477-018-0210-1\" aria-label=\"Article reference 13\" data-doi=\"10.1038\/s41477-018-0210-1\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30061748\" aria-label=\"PubMed reference 13\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 13\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Demography%20and%20its%20effects%20on%20genomic%20variation%20in%20crop%20domestication&amp;journal=Nat.%20Plants&amp;doi=10.1038%2Fs41477-018-0210-1&amp;volume=4&amp;pages=512-520&amp;publication_year=2018&amp;author=Gaut%2CBS&amp;author=Seymour%2CDK&amp;author=Liu%2CQ&amp;author=Zhou%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"14.\">\n<p class=\"c-article-references__text\" id=\"ref-CR14\">Wellenreuther, M., M\u00e9rot, C., Berdan, E. &amp; Bernatchez, L. Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification. Mol. Ecol. <b>28<\/b>, 1203\u20131209 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1111\/mec.15066\" data-track-item_id=\"10.1111\/mec.15066\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1111%2Fmec.15066\" aria-label=\"Article reference 14\" data-doi=\"10.1111\/mec.15066\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30834648\" aria-label=\"PubMed reference 14\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 14\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Going%20beyond%20SNPs%3A%20the%20role%20of%20structural%20genomic%20variants%20in%20adaptive%20evolution%20and%20species%20diversification&amp;journal=Mol.%20Ecol.&amp;doi=10.1111%2Fmec.15066&amp;volume=28&amp;pages=1203-1209&amp;publication_year=2019&amp;author=Wellenreuther%2CM&amp;author=M%C3%A9rot%2CC&amp;author=Berdan%2CE&amp;author=Bernatchez%2CL\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"15.\">\n<p class=\"c-article-references__text\" id=\"ref-CR15\">Huang, K. &amp; Rieseberg, L. H. Frequency, origins, and evolutionary role of chromosomal inversions in plants. Front. Plant Sci. <b>11<\/b>, 296 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.3389\/fpls.2020.00296\" data-track-item_id=\"10.3389\/fpls.2020.00296\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.3389%2Ffpls.2020.00296\" aria-label=\"Article reference 15\" data-doi=\"10.3389\/fpls.2020.00296\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32256515\" aria-label=\"PubMed reference 15\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7093584\" aria-label=\"PubMed Central reference 15\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 15\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Frequency%2C%20origins%2C%20and%20evolutionary%20role%20of%20chromosomal%20inversions%20in%20plants&amp;journal=Front.%20Plant%20Sci.&amp;doi=10.3389%2Ffpls.2020.00296&amp;volume=11&amp;publication_year=2020&amp;author=Huang%2CK&amp;author=Rieseberg%2CLH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"16.\">\n<p class=\"c-article-references__text\" id=\"ref-CR16\">Kirkpatrick, M. &amp; Barton, N. Chromosome inversions, local adaptation and speciation. Genetics <b>173<\/b>, 419\u2013434 (2006).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1534\/genetics.105.047985\" data-track-item_id=\"10.1534\/genetics.105.047985\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1534%2Fgenetics.105.047985\" aria-label=\"Article reference 16\" data-doi=\"10.1534\/genetics.105.047985\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD28XlvF2it7s%3D\" aria-label=\"CAS reference 16\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=16204214\" aria-label=\"PubMed reference 16\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1461441\" aria-label=\"PubMed Central reference 16\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 16\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Chromosome%20inversions%2C%20local%20adaptation%20and%20speciation&amp;journal=Genetics&amp;doi=10.1534%2Fgenetics.105.047985&amp;volume=173&amp;pages=419-434&amp;publication_year=2006&amp;author=Kirkpatrick%2CM&amp;author=Barton%2CN\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"17.\">\n<p class=\"c-article-references__text\" id=\"ref-CR17\">Zhang, X. et al. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nat. Genet. <b>53<\/b>, 1250\u20131259 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41588-021-00895-y\" data-track-item_id=\"10.1038\/s41588-021-00895-y\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41588-021-00895-y\" aria-label=\"Article reference 17\" data-doi=\"10.1038\/s41588-021-00895-y\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXhsFOntLnJ\" aria-label=\"CAS reference 17\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=34267370\" aria-label=\"PubMed reference 17\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8346365\" aria-label=\"PubMed Central reference 17\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 17\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Haplotype-resolved%20genome%20assembly%20provides%20insights%20into%20evolutionary%20history%20of%20the%20tea%20plant%20Camellia%20sinensis&amp;journal=Nat.%20Genet.&amp;doi=10.1038%2Fs41588-021-00895-y&amp;volume=53&amp;pages=1250-1259&amp;publication_year=2021&amp;author=Zhang%2CX\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"18.\">\n<p class=\"c-article-references__text\" id=\"ref-CR18\">Sim\u00e3o, F. A., Waterhouse, R. M., Panagiotis, I., Kriventseva, E. V. &amp; Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics <b>31<\/b>, 3210\u20133212 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btv351\" data-track-item_id=\"10.1093\/bioinformatics\/btv351\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtv351\" aria-label=\"Article reference 18\" data-doi=\"10.1093\/bioinformatics\/btv351\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=26059717\" aria-label=\"PubMed reference 18\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 18\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=BUSCO%3A%20assessing%20genome%20assembly%20and%20annotation%20completeness%20with%20single-copy%20orthologs&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtv351&amp;volume=31&amp;pages=3210-3212&amp;publication_year=2015&amp;author=Sim%C3%A3o%2CFA&amp;author=Waterhouse%2CRM&amp;author=Panagiotis%2CI&amp;author=Kriventseva%2CEV&amp;author=Zdobnov%2CEM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"19.\">\n<p class=\"c-article-references__text\" id=\"ref-CR19\">Ou, S., Chen, J. &amp; Jiang, N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. <b>46<\/b>, e126 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30107434\" aria-label=\"PubMed reference 19\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6265445\" aria-label=\"PubMed Central reference 19\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 19\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Assessing%20genome%20assembly%20quality%20using%20the%20LTR%20Assembly%20Index%20%28LAI%29&amp;journal=Nucleic%20Acids%20Res.&amp;volume=46&amp;publication_year=2018&amp;author=Ou%2CS&amp;author=Chen%2CJ&amp;author=Jiang%2CN\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"20.\">\n<p class=\"c-article-references__text\" id=\"ref-CR20\">Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. <b>23<\/b>, 258 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/s13059-022-02823-7\" data-track-item_id=\"10.1186\/s13059-022-02823-7\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s13059-022-02823-7\" aria-label=\"Article reference 20\" data-doi=\"10.1186\/s13059-022-02823-7\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38XjtF2kt7rM\" aria-label=\"CAS reference 20\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=36522651\" aria-label=\"PubMed reference 20\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9753292\" aria-label=\"PubMed Central reference 20\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 20\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Automated%20assembly%20scaffolding%20using%20RagTag%20elevates%20a%20new%20tomato%20system%20for%20high-throughput%20genome%20editing&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fs13059-022-02823-7&amp;volume=23&amp;publication_year=2022&amp;author=Alonge%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"21.\">\n<p class=\"c-article-references__text\" id=\"ref-CR21\">Li, A. et al. A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa. Hortic. Res. <b>7<\/b>, 194 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41438-020-00417-7\" data-track-item_id=\"10.1038\/s41438-020-00417-7\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41438-020-00417-7\" aria-label=\"Article reference 21\" data-doi=\"10.1038\/s41438-020-00417-7\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXisVGktr%2FN\" aria-label=\"CAS reference 21\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33328470\" aria-label=\"PubMed reference 21\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7705661\" aria-label=\"PubMed Central reference 21\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 21\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20chromosome-scale%20genome%20assembly%20of%20a%20diploid%20alfalfa%2C%20the%20progenitor%20of%20autotetraploid%20alfalfa&amp;journal=Hortic.%20Res.&amp;doi=10.1038%2Fs41438-020-00417-7&amp;volume=7&amp;publication_year=2020&amp;author=Li%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"22.\">\n<p class=\"c-article-references__text\" id=\"ref-CR22\">Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. <b>42<\/b>, D222\u2013D230 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkt1223\" data-track-item_id=\"10.1093\/nar\/gkt1223\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkt1223\" aria-label=\"Article reference 22\" data-doi=\"10.1093\/nar\/gkt1223\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXos1al\" aria-label=\"CAS reference 22\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24288371\" aria-label=\"PubMed reference 22\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 22\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Pfam%3A%20the%20protein%20families%20database&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkt1223&amp;volume=42&amp;pages=D222-D230&amp;publication_year=2014&amp;author=Finn%2CRD\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"23.\">\n<p class=\"c-article-references__text\" id=\"ref-CR23\">Cantalapiedra, C. P., Hern\u00e1ndez-Plaza, A., Letunic, I., Bork, P. &amp; Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. <b>38<\/b>, 5825\u20135829 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/molbev\/msab293\" data-track-item_id=\"10.1093\/molbev\/msab293\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fmolbev%2Fmsab293\" aria-label=\"Article reference 23\" data-doi=\"10.1093\/molbev\/msab293\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38Xhslyrt78%3D\" aria-label=\"CAS reference 23\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=34597405\" aria-label=\"PubMed reference 23\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8662613\" aria-label=\"PubMed Central reference 23\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 23\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=eggNOG-mapper%20v2%3A%20functional%20annotation%2C%20orthology%20assignments%2C%20and%20domain%20prediction%20at%20the%20metagenomic%20scale&amp;journal=Mol.%20Biol.%20Evol.&amp;doi=10.1093%2Fmolbev%2Fmsab293&amp;volume=38&amp;pages=5825-5829&amp;publication_year=2021&amp;author=Cantalapiedra%2CCP&amp;author=Hern%C3%A1ndez-Plaza%2CA&amp;author=Letunic%2CI&amp;author=Bork%2CP&amp;author=Huerta-Cepas%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"24.\">\n<p class=\"c-article-references__text\" id=\"ref-CR24\">Zhou, S., Chen, Q., Li, X. &amp; Li, Y. MAP65-1 is required for the depolymerization and reorganization of cortical microtubules in the response to salt stress in Arabidopsis. Plant Sci. <b>264<\/b>, 112\u2013121 (2017).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.plantsci.2017.09.004\" data-track-item_id=\"10.1016\/j.plantsci.2017.09.004\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.plantsci.2017.09.004\" aria-label=\"Article reference 24\" data-doi=\"10.1016\/j.plantsci.2017.09.004\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhsFKjurnI\" aria-label=\"CAS reference 24\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=28969791\" aria-label=\"PubMed reference 24\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 24\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=MAP65-1%20is%20required%20for%20the%20depolymerization%20and%20reorganization%20of%20cortical%20microtubules%20in%20the%20response%20to%20salt%20stress%20in%20Arabidopsis&amp;journal=Plant%20Sci.&amp;doi=10.1016%2Fj.plantsci.2017.09.004&amp;volume=264&amp;pages=112-121&amp;publication_year=2017&amp;author=Zhou%2CS&amp;author=Chen%2CQ&amp;author=Li%2CX&amp;author=Li%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"25.\">\n<p class=\"c-article-references__text\" id=\"ref-CR25\">Liang, M. et al. Comprehensive analyses of microtubule-associated protein MAP65 family genes in Cucurbitaceae and CsaMAP65s expression profiles in cucumber. J. Appl. Genet. <b>64<\/b>, 393\u2013408 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1007\/s13353-023-00761-z\" data-track-item_id=\"10.1007\/s13353-023-00761-z\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/s13353-023-00761-z\" aria-label=\"Article reference 25\" data-doi=\"10.1007\/s13353-023-00761-z\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXhtFOlsL%2FK\" aria-label=\"CAS reference 25\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37219731\" aria-label=\"PubMed reference 25\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 25\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Comprehensive%20analyses%20of%20microtubule-associated%20protein%20MAP65%20family%20genes%20in%20Cucurbitaceae%20and%20CsaMAP65s%20expression%20profiles%20in%20cucumber&amp;journal=J.%20Appl.%20Genet.&amp;doi=10.1007%2Fs13353-023-00761-z&amp;volume=64&amp;pages=393-408&amp;publication_year=2023&amp;author=Liang%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"26.\">\n<p class=\"c-article-references__text\" id=\"ref-CR26\">Dwiningsih, Y. &amp; Al-Kahtani, J. Genome-wide association study of complex traits in maize detects genomic regions and genes for increasing grain yield and grain quality. Adv. Sustain. Sci. Eng. Technol. <b>4<\/b>, 0220209 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 26\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Genome-wide%20association%20study%20of%20complex%20traits%20in%20maize%20detects%20genomic%20regions%20and%20genes%20for%20increasing%20grain%20yield%20and%20grain%20quality&amp;journal=Adv.%20Sustain.%20Sci.%20Eng.%20Technol.&amp;volume=4&amp;publication_year=2022&amp;author=Dwiningsih%2CY&amp;author=Al-Kahtani%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"27.\">\n<p class=\"c-article-references__text\" id=\"ref-CR27\">Liu, R. et al. GWAS analysis and QTL identification of fiber quality traits and yield components in upland cotton using enriched high-density SNP markers. Front. Plant Sci. <b>13<\/b>, 1067 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.3389\/fpls.2018.01067\" data-track-item_id=\"10.3389\/fpls.2018.01067\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.3389%2Ffpls.2018.01067\" aria-label=\"Article reference 27\" data-doi=\"10.3389\/fpls.2018.01067\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 27\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=GWAS%20analysis%20and%20QTL%20identification%20of%20fiber%20quality%20traits%20and%20yield%20components%20in%20upland%20cotton%20using%20enriched%20high-density%20SNP%20markers&amp;journal=Front.%20Plant%20Sci.&amp;doi=10.3389%2Ffpls.2018.01067&amp;volume=13&amp;publication_year=2018&amp;author=Liu%2CR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"28.\">\n<p class=\"c-article-references__text\" id=\"ref-CR28\">Kephart, K. D., Buxton, D. &amp; Hill, R. Jr Digestibility and cell\u2010wall components of alfalfa following selection for divergent herbage lignin concentration. Crop Sci. <b>30<\/b>, 207\u2013212 (1990).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.2135\/cropsci1990.0011183X003000010045x\" data-track-item_id=\"10.2135\/cropsci1990.0011183X003000010045x\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.2135%2Fcropsci1990.0011183X003000010045x\" aria-label=\"Article reference 28\" data-doi=\"10.2135\/cropsci1990.0011183X003000010045x\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 28\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Digestibility%20and%20cell%E2%80%90wall%20components%20of%20alfalfa%20following%20selection%20for%20divergent%20herbage%20lignin%20concentration&amp;journal=Crop%20Sci.&amp;doi=10.2135%2Fcropsci1990.0011183X003000010045x&amp;volume=30&amp;pages=207-212&amp;publication_year=1990&amp;author=Kephart%2CKD&amp;author=Buxton%2CD&amp;author=Hill%2CR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"29.\">\n<p class=\"c-article-references__text\" id=\"ref-CR29\">Han, R.-H., Lu, X.-S., Gao, G.-J. &amp; Yang, X.-J. Analysis of the principal components and the subordinate function of alfalfa drought resistance. Acta Agrestia Sin. <b>14<\/b>, 142 (2006).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 29\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Analysis%20of%20the%20principal%20components%20and%20the%20subordinate%20function%20of%20alfalfa%20drought%20resistance&amp;journal=Acta%20Agrestia%20Sin.&amp;volume=14&amp;publication_year=2006&amp;author=Han%2CR-H&amp;author=Lu%2CX-S&amp;author=Gao%2CG-J&amp;author=Yang%2CX-J\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"30.\">\n<p class=\"c-article-references__text\" id=\"ref-CR30\">Reinecke, D. M. et al. Gibberellin 3-oxidase gene expression patterns influence gibberellin biosynthesis, growth, and development in pea. Plant Physiol. <b>163<\/b>, 929\u2013945 (2013).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1104\/pp.113.225987\" data-track-item_id=\"10.1104\/pp.113.225987\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1104%2Fpp.113.225987\" aria-label=\"Article reference 30\" data-doi=\"10.1104\/pp.113.225987\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3sXhs1OjsLvO\" aria-label=\"CAS reference 30\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=23979969\" aria-label=\"PubMed reference 30\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3793069\" aria-label=\"PubMed Central reference 30\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 30\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Gibberellin%203-oxidase%20gene%20expression%20patterns%20influence%20gibberellin%20biosynthesis%2C%20growth%2C%20and%20development%20in%20pea&amp;journal=Plant%20Physiol.&amp;doi=10.1104%2Fpp.113.225987&amp;volume=163&amp;pages=929-945&amp;publication_year=2013&amp;author=Reinecke%2CDM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"31.\">\n<p class=\"c-article-references__text\" id=\"ref-CR31\">Wu, H., Bai, B., Lu, X. &amp; Li, H. A gibberellin-deficient maize mutant exhibits altered plant height, stem strength and drought tolerance. Plant Cell Rep. <b>42<\/b>, 1687\u20131699 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1007\/s00299-023-03054-1\" data-track-item_id=\"10.1007\/s00299-023-03054-1\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/s00299-023-03054-1\" aria-label=\"Article reference 31\" data-doi=\"10.1007\/s00299-023-03054-1\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXhsFejt7%2FN\" aria-label=\"CAS reference 31\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37479884\" aria-label=\"PubMed reference 31\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 31\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20gibberellin-deficient%20maize%20mutant%20exhibits%20altered%20plant%20height%2C%20stem%20strength%20and%20drought%20tolerance&amp;journal=Plant%20Cell%20Rep.&amp;doi=10.1007%2Fs00299-023-03054-1&amp;volume=42&amp;pages=1687-1699&amp;publication_year=2023&amp;author=Wu%2CH&amp;author=Bai%2CB&amp;author=Lu%2CX&amp;author=Li%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"32.\">\n<p class=\"c-article-references__text\" id=\"ref-CR32\">Ameur, A. Goodbye reference, hello genome graphs. Nat. Biotechnol. <b>37<\/b>, 866\u2013868 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41587-019-0199-7\" data-track-item_id=\"10.1038\/s41587-019-0199-7\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41587-019-0199-7\" aria-label=\"Article reference 32\" data-doi=\"10.1038\/s41587-019-0199-7\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhsFWqt7fF\" aria-label=\"CAS reference 32\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31375808\" aria-label=\"PubMed reference 32\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 32\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Goodbye%20reference%2C%20hello%20genome%20graphs&amp;journal=Nat.%20Biotechnol.&amp;doi=10.1038%2Fs41587-019-0199-7&amp;volume=37&amp;pages=866-868&amp;publication_year=2019&amp;author=Ameur%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"33.\">\n<p class=\"c-article-references__text\" id=\"ref-CR33\">Garrison, E. et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat. Biotechnol. <b>36<\/b>, 875\u2013879 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nbt.4227\" data-track-item_id=\"10.1038\/nbt.4227\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnbt.4227\" aria-label=\"Article reference 33\" data-doi=\"10.1038\/nbt.4227\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1cXhsFChurbJ\" aria-label=\"CAS reference 33\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30125266\" aria-label=\"PubMed reference 33\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6126949\" aria-label=\"PubMed Central reference 33\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 33\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Variation%20graph%20toolkit%20improves%20read%20mapping%20by%20representing%20genetic%20variation%20in%20the%20reference&amp;journal=Nat.%20Biotechnol.&amp;doi=10.1038%2Fnbt.4227&amp;volume=36&amp;pages=875-879&amp;publication_year=2018&amp;author=Garrison%2CE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"34.\">\n<p class=\"c-article-references__text\" id=\"ref-CR34\">Qin, P. et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell <b>184<\/b>, 3542\u20133558.e16 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2021.04.046\" data-track-item_id=\"10.1016\/j.cell.2021.04.046\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2021.04.046\" aria-label=\"Article reference 34\" data-doi=\"10.1016\/j.cell.2021.04.046\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXhtlSrtr%2FM\" aria-label=\"CAS reference 34\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=34051138\" aria-label=\"PubMed reference 34\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 34\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Pan-genome%20analysis%20of%2033%20genetically%20diverse%20rice%20accessions%20reveals%20hidden%20genomic%20variations&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2021.04.046&amp;volume=184&amp;pages=3542-3558.e16&amp;publication_year=2021&amp;author=Qin%2CP\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"35.\">\n<p class=\"c-article-references__text\" id=\"ref-CR35\">Alonge, M. et al. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell <b>182<\/b>, 145\u2013161.e23 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2020.05.021\" data-track-item_id=\"10.1016\/j.cell.2020.05.021\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2020.05.021\" aria-label=\"Article reference 35\" data-doi=\"10.1016\/j.cell.2020.05.021\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhtFykt7fN\" aria-label=\"CAS reference 35\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32553272\" aria-label=\"PubMed reference 35\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7354227\" aria-label=\"PubMed Central reference 35\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 35\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Major%20impacts%20of%20widespread%20structural%20variation%20on%20gene%20expression%20and%20crop%20improvement%20in%20tomato&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2020.05.021&amp;volume=182&amp;pages=145-161.e23&amp;publication_year=2020&amp;author=Alonge%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"36.\">\n<p class=\"c-article-references__text\" id=\"ref-CR36\">He, Q. et al. A graph-based genome and pan-genome variation of the model plant Setaria. Nat. Genet. <b>55<\/b>, 1232\u20131242 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41588-023-01423-w\" data-track-item_id=\"10.1038\/s41588-023-01423-w\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41588-023-01423-w\" aria-label=\"Article reference 36\" data-doi=\"10.1038\/s41588-023-01423-w\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXhtF2itbrK\" aria-label=\"CAS reference 36\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37291196\" aria-label=\"PubMed reference 36\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10335933\" aria-label=\"PubMed Central reference 36\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 36\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20graph-based%20genome%20and%20pan-genome%20variation%20of%20the%20model%20plant%20Setaria&amp;journal=Nat.%20Genet.&amp;doi=10.1038%2Fs41588-023-01423-w&amp;volume=55&amp;pages=1232-1242&amp;publication_year=2023&amp;author=He%2CQ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"37.\">\n<p class=\"c-article-references__text\" id=\"ref-CR37\">Huang, Y. et al. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat. Genet. <b>55<\/b>, 1964\u20131975 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41588-023-01516-6\" data-track-item_id=\"10.1038\/s41588-023-01516-6\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41588-023-01516-6\" aria-label=\"Article reference 37\" data-doi=\"10.1038\/s41588-023-01516-6\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXitVeqs77L\" aria-label=\"CAS reference 37\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37783780\" aria-label=\"PubMed reference 37\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 37\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Pangenome%20analysis%20provides%20insight%20into%20the%20evolution%20of%20the%20orange%20subfamily%20and%20a%20key%20gene%20for%20citric%20acid%20accumulation%20in%20citrus%20fruits&amp;journal=Nat.%20Genet.&amp;doi=10.1038%2Fs41588-023-01516-6&amp;volume=55&amp;pages=1964-1975&amp;publication_year=2023&amp;author=Huang%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"38.\">\n<p class=\"c-article-references__text\" id=\"ref-CR38\">Liu, Y. et al. Pan-genome of wild and cultivated soybeans. Cell <b>182<\/b>, 162\u2013176.e13 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2020.05.023\" data-track-item_id=\"10.1016\/j.cell.2020.05.023\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2020.05.023\" aria-label=\"Article reference 38\" data-doi=\"10.1016\/j.cell.2020.05.023\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhtFyktrjI\" aria-label=\"CAS reference 38\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32553274\" aria-label=\"PubMed reference 38\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 38\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Pan-genome%20of%20wild%20and%20cultivated%20soybeans&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2020.05.023&amp;volume=182&amp;pages=162-176.e13&amp;publication_year=2020&amp;author=Liu%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"39.\">\n<p class=\"c-article-references__text\" id=\"ref-CR39\">Hu, J. et al. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. Plant Cell <b>20<\/b>, 320\u2013336 (2008).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1105\/tpc.107.057752\" data-track-item_id=\"10.1105\/tpc.107.057752\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1105%2Ftpc.107.057752\" aria-label=\"Article reference 39\" data-doi=\"10.1105\/tpc.107.057752\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1cXkslSitb8%3D\" aria-label=\"CAS reference 39\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=18310462\" aria-label=\"PubMed reference 39\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2276448\" aria-label=\"PubMed Central reference 39\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 39\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Potential%20sites%20of%20bioactive%20gibberellin%20production%20during%20reproductive%20growth%20in%20Arabidopsis&amp;journal=Plant%20Cell&amp;doi=10.1105%2Ftpc.107.057752&amp;volume=20&amp;pages=320-336&amp;publication_year=2008&amp;author=Hu%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"40.\">\n<p class=\"c-article-references__text\" id=\"ref-CR40\">Sun, H. et al. Gibberellins inhibit flavonoid biosynthesis and promote nitrogen metabolism in Medicago truncatula. Int. J. Mol. Sci. <b>22<\/b>, 9291 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.3390\/ijms22179291\" data-track-item_id=\"10.3390\/ijms22179291\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.3390%2Fijms22179291\" aria-label=\"Article reference 40\" data-doi=\"10.3390\/ijms22179291\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXitlCls7rF\" aria-label=\"CAS reference 40\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=34502200\" aria-label=\"PubMed reference 40\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8431309\" aria-label=\"PubMed Central reference 40\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 40\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Gibberellins%20inhibit%20flavonoid%20biosynthesis%20and%20promote%20nitrogen%20metabolism%20in%20Medicago%20truncatula&amp;journal=Int.%20J.%20Mol.%20Sci.&amp;doi=10.3390%2Fijms22179291&amp;volume=22&amp;publication_year=2021&amp;author=Sun%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"41.\">\n<p class=\"c-article-references__text\" id=\"ref-CR41\">Dalmadi, \u00c1. et al. Dwarf plants of diploid Medicago sativa carry a mutation in the gibberellin 3-\u03b2-hydroxylase gene. Plant Cell Rep. <b>27<\/b>, 1271\u20131279 (2008).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1007\/s00299-008-0546-5\" data-track-item_id=\"10.1007\/s00299-008-0546-5\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/s00299-008-0546-5\" aria-label=\"Article reference 41\" data-doi=\"10.1007\/s00299-008-0546-5\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1cXotVyksb8%3D\" aria-label=\"CAS reference 41\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=18504589\" aria-label=\"PubMed reference 41\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 41\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Dwarf%20plants%20of%20diploid%20Medicago%20sativa%20carry%20a%20mutation%20in%20the%20gibberellin%203-%CE%B2-hydroxylase%20gene&amp;journal=Plant%20Cell%20Rep.&amp;doi=10.1007%2Fs00299-008-0546-5&amp;volume=27&amp;pages=1271-1279&amp;publication_year=2008&amp;author=Dalmadi%2C%C3%81\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"42.\">\n<p class=\"c-article-references__text\" id=\"ref-CR42\">Israelsson, M., Mellerowicz, E., Chono, M., Gullberg, J. &amp; Moritz, T. Cloning and overproduction of gibberellin 3-oxidase in hybrid aspen trees. Effects on gibberellin homeostasis and development. Plant Physiol. <b>135<\/b>, 221\u2013230 (2004).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1104\/pp.104.038935\" data-track-item_id=\"10.1104\/pp.104.038935\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1104%2Fpp.104.038935\" aria-label=\"Article reference 42\" data-doi=\"10.1104\/pp.104.038935\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD2cXkt12nurw%3D\" aria-label=\"CAS reference 42\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=15122019\" aria-label=\"PubMed reference 42\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC429357\" aria-label=\"PubMed Central reference 42\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 42\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Cloning%20and%20overproduction%20of%20gibberellin%203-oxidase%20in%20hybrid%20aspen%20trees.%20Effects%20on%20gibberellin%20homeostasis%20and%20development&amp;journal=Plant%20Physiol.&amp;doi=10.1104%2Fpp.104.038935&amp;volume=135&amp;pages=221-230&amp;publication_year=2004&amp;author=Israelsson%2CM&amp;author=Mellerowicz%2CE&amp;author=Chono%2CM&amp;author=Gullberg%2CJ&amp;author=Moritz%2CT\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"43.\">\n<p class=\"c-article-references__text\" id=\"ref-CR43\">Zheng, L. et al. From model to alfalfa: gene editing to obtain semidwarf and prostrate growth habits. Crop J. <b>10<\/b>, 932\u2013941 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cj.2021.11.008\" data-track-item_id=\"10.1016\/j.cj.2021.11.008\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cj.2021.11.008\" aria-label=\"Article reference 43\" data-doi=\"10.1016\/j.cj.2021.11.008\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 43\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=From%20model%20to%20alfalfa%3A%20gene%20editing%20to%20obtain%20semidwarf%20and%20prostrate%20growth%20habits&amp;journal=Crop%20J.&amp;doi=10.1016%2Fj.cj.2021.11.008&amp;volume=10&amp;pages=932-941&amp;publication_year=2022&amp;author=Zheng%2CL\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"44.\">\n<p class=\"c-article-references__text\" id=\"ref-CR44\">He, X. et al. Accuracy of genomic selection for alfalfa biomass yield in two full-sib populations. Front. Plant Sci. <b>13<\/b>, 1037272 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.3389\/fpls.2022.1037272\" data-track-item_id=\"10.3389\/fpls.2022.1037272\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.3389%2Ffpls.2022.1037272\" aria-label=\"Article reference 44\" data-doi=\"10.3389\/fpls.2022.1037272\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=36388566\" aria-label=\"PubMed reference 44\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9650308\" aria-label=\"PubMed Central reference 44\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 44\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Accuracy%20of%20genomic%20selection%20for%20alfalfa%20biomass%20yield%20in%20two%20full-sib%20populations&amp;journal=Front.%20Plant%20Sci.&amp;doi=10.3389%2Ffpls.2022.1037272&amp;volume=13&amp;publication_year=2022&amp;author=He%2CX\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"45.\">\n<p class=\"c-article-references__text\" id=\"ref-CR45\">Zhang, F. et al. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. Mol. Plant <b>17<\/b>, 867\u2013883 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.molp.2024.04.013\" data-track-item_id=\"10.1016\/j.molp.2024.04.013\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.molp.2024.04.013\" aria-label=\"Article reference 45\" data-doi=\"10.1016\/j.molp.2024.04.013\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXhtFOiurbJ\" aria-label=\"CAS reference 45\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=38678365\" aria-label=\"PubMed reference 45\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 45\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Evolutionary%20genomics%20of%20climatic%20adaptation%20and%20resilience%20to%20climate%20change%20in%20alfalfa&amp;journal=Mol.%20Plant&amp;doi=10.1016%2Fj.molp.2024.04.013&amp;volume=17&amp;pages=867-883&amp;publication_year=2024&amp;author=Zhang%2CF\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"46.\">\n<p class=\"c-article-references__text\" id=\"ref-CR46\">Li, H. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics <b>25<\/b>, 1754\u20131760 (2009).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btp324\" data-track-item_id=\"10.1093\/bioinformatics\/btp324\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtp324\" aria-label=\"Article reference 46\" data-doi=\"10.1093\/bioinformatics\/btp324\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1MXot1Cjtbo%3D\" aria-label=\"CAS reference 46\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=19451168\" aria-label=\"PubMed reference 46\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2705234\" aria-label=\"PubMed Central reference 46\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 46\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Fast%20and%20accurate%20short%20read%20alignment%20with%20Burrows%E2%80%93Wheeler%20transform&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtp324&amp;volume=25&amp;pages=1754-1760&amp;publication_year=2009&amp;author=Li%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"47.\">\n<p class=\"c-article-references__text\" id=\"ref-CR47\">Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics <b>25<\/b>, 2078\u20132079 (2009).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btp352\" data-track-item_id=\"10.1093\/bioinformatics\/btp352\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtp352\" aria-label=\"Article reference 47\" data-doi=\"10.1093\/bioinformatics\/btp352\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=19505943\" aria-label=\"PubMed reference 47\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2723002\" aria-label=\"PubMed Central reference 47\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 47\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20sequence%20alignment%2Fmap%20format%20and%20SAMtools&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtp352&amp;volume=25&amp;pages=2078-2079&amp;publication_year=2009&amp;author=Li%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"48.\">\n<p class=\"c-article-references__text\" id=\"ref-CR48\">Danecek, P. et al. The variant call format and VCFtools. Bioinformatics <b>27<\/b>, 2156\u20132158 (2011).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btr330\" data-track-item_id=\"10.1093\/bioinformatics\/btr330\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtr330\" aria-label=\"Article reference 48\" data-doi=\"10.1093\/bioinformatics\/btr330\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3MXptFCqt7w%3D\" aria-label=\"CAS reference 48\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=21653522\" aria-label=\"PubMed reference 48\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3137218\" aria-label=\"PubMed Central reference 48\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 48\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20variant%20call%20format%20and%20VCFtools&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtr330&amp;volume=27&amp;pages=2156-2158&amp;publication_year=2011&amp;author=Danecek%2CP\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"49.\">\n<p class=\"c-article-references__text\" id=\"ref-CR49\">Price, M. N., Dehal, P. S. &amp; Arkin, A. P. FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments. PLoS ONE <b>5<\/b>, e9490 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pone.0009490\" data-track-item_id=\"10.1371\/journal.pone.0009490\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pone.0009490\" aria-label=\"Article reference 49\" data-doi=\"10.1371\/journal.pone.0009490\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20224823\" aria-label=\"PubMed reference 49\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2835736\" aria-label=\"PubMed Central reference 49\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 49\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=FastTree%202%20%E2%80%93%20approximately%20maximum-likelihood%20trees%20for%20large%20alignments&amp;journal=PLoS%20ONE&amp;doi=10.1371%2Fjournal.pone.0009490&amp;volume=5&amp;publication_year=2010&amp;author=Price%2CMN&amp;author=Dehal%2CPS&amp;author=Arkin%2CAP\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"50.\">\n<p class=\"c-article-references__text\" id=\"ref-CR50\">Alexander, D. H. &amp; Lange, K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics <b>12<\/b>, 246 (2011).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/1471-2105-12-246\" data-track-item_id=\"10.1186\/1471-2105-12-246\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/1471-2105-12-246\" aria-label=\"Article reference 50\" data-doi=\"10.1186\/1471-2105-12-246\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=21682921\" aria-label=\"PubMed reference 50\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3146885\" aria-label=\"PubMed Central reference 50\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 50\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Enhancements%20to%20the%20ADMIXTURE%20algorithm%20for%20individual%20ancestry%20estimation&amp;journal=BMC%20Bioinformatics&amp;doi=10.1186%2F1471-2105-12-246&amp;volume=12&amp;publication_year=2011&amp;author=Alexander%2CDH&amp;author=Lange%2CK\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"51.\">\n<p class=\"c-article-references__text\" id=\"ref-CR51\">Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. <b>3<\/b>, 95\u201398 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cels.2016.07.002\" data-track-item_id=\"10.1016\/j.cels.2016.07.002\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cels.2016.07.002\" aria-label=\"Article reference 51\" data-doi=\"10.1016\/j.cels.2016.07.002\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhtFKksbk%3D\" aria-label=\"CAS reference 51\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27467249\" aria-label=\"PubMed reference 51\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5846465\" aria-label=\"PubMed Central reference 51\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 51\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Juicer%20provides%20a%20one-click%20system%20for%20analyzing%20loop-resolution%20Hi-C%20experiments&amp;journal=Cell%20Syst.&amp;doi=10.1016%2Fj.cels.2016.07.002&amp;volume=3&amp;pages=95-98&amp;publication_year=2016&amp;author=Durand%2CNC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"52.\">\n<p class=\"c-article-references__text\" id=\"ref-CR52\">Zhang, X., Zhang, S., Zhao, Q., Ming, R. &amp; Tang, H. Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat. Plants <b>5<\/b>, 833\u2013845 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41477-019-0487-8\" data-track-item_id=\"10.1038\/s41477-019-0487-8\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41477-019-0487-8\" aria-label=\"Article reference 52\" data-doi=\"10.1038\/s41477-019-0487-8\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhsFCmsr3O\" aria-label=\"CAS reference 52\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31383970\" aria-label=\"PubMed reference 52\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 52\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Assembly%20of%20allele-aware%2C%20chromosomal-scale%20autopolyploid%20genomes%20based%20on%20Hi-C%20data&amp;journal=Nat.%20Plants&amp;doi=10.1038%2Fs41477-019-0487-8&amp;volume=5&amp;pages=833-845&amp;publication_year=2019&amp;author=Zhang%2CX&amp;author=Zhang%2CS&amp;author=Zhao%2CQ&amp;author=Ming%2CR&amp;author=Tang%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"53.\">\n<p class=\"c-article-references__text\" id=\"ref-CR53\">Zhang, J. et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat. Genet. <b>50<\/b>, 1565\u20131573 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41588-018-0237-2\" data-track-item_id=\"10.1038\/s41588-018-0237-2\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41588-018-0237-2\" aria-label=\"Article reference 53\" data-doi=\"10.1038\/s41588-018-0237-2\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1cXitVCitL3F\" aria-label=\"CAS reference 53\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30297971\" aria-label=\"PubMed reference 53\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 53\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Allele-defined%20genome%20of%20the%20autopolyploid%20sugarcane%20Saccharum%20spontaneum%20L.&amp;journal=Nat.%20Genet.&amp;doi=10.1038%2Fs41588-018-0237-2&amp;volume=50&amp;pages=1565-1573&amp;publication_year=2018&amp;author=Zhang%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"54.\">\n<p class=\"c-article-references__text\" id=\"ref-CR54\">Wu, T. D. &amp; Watanabe, C. K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics <b>21<\/b>, 1859 (2005).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/bti310\" data-track-item_id=\"10.1093\/bioinformatics\/bti310\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbti310\" aria-label=\"Article reference 54\" data-doi=\"10.1093\/bioinformatics\/bti310\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD2MXjsl2ntLw%3D\" aria-label=\"CAS reference 54\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=15728110\" aria-label=\"PubMed reference 54\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 54\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=GMAP%3A%20a%20genomic%20mapping%20and%20alignment%20program%20for%20mRNA%20and%20EST%20sequences&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbti310&amp;volume=21&amp;publication_year=2005&amp;author=Wu%2CTD&amp;author=Watanabe%2CCK\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"55.\">\n<p class=\"c-article-references__text\" id=\"ref-CR55\">Tang, H. et al. An improved genome release (Version Mt4.0) for the model legume Medicago truncatula. BMC Genomics <b>15<\/b>, 312 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/1471-2164-15-312\" data-track-item_id=\"10.1186\/1471-2164-15-312\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/1471-2164-15-312\" aria-label=\"Article reference 55\" data-doi=\"10.1186\/1471-2164-15-312\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24767513\" aria-label=\"PubMed reference 55\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4234490\" aria-label=\"PubMed Central reference 55\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 55\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=An%20improved%20genome%20release%20%28Version%20Mt4.0%29%20for%20the%20model%20legume%20Medicago%20truncatula.&amp;journal=BMC%20Genomics&amp;doi=10.1186%2F1471-2164-15-312&amp;volume=15&amp;publication_year=2014&amp;author=Tang%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"56.\">\n<p class=\"c-article-references__text\" id=\"ref-CR56\">Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. <b>40<\/b>, e49 (2012).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkr1293\" data-track-item_id=\"10.1093\/nar\/gkr1293\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkr1293\" aria-label=\"Article reference 56\" data-doi=\"10.1093\/nar\/gkr1293\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38Xls1SmsL0%3D\" aria-label=\"CAS reference 56\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=22217600\" aria-label=\"PubMed reference 56\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3326336\" aria-label=\"PubMed Central reference 56\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 56\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=MCScanX%3A%20a%20toolkit%20for%20detection%20and%20evolutionary%20analysis%20of%20gene%20synteny%20and%20collinearity&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkr1293&amp;volume=40&amp;publication_year=2012&amp;author=Wang%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"57.\">\n<p class=\"c-article-references__text\" id=\"ref-CR57\">Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. &amp; Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods <b>18<\/b>, 170\u2013175 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41592-020-01056-5\" data-track-item_id=\"10.1038\/s41592-020-01056-5\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41592-020-01056-5\" aria-label=\"Article reference 57\" data-doi=\"10.1038\/s41592-020-01056-5\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXis1OntL0%3D\" aria-label=\"CAS reference 57\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33526886\" aria-label=\"PubMed reference 57\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7961889\" aria-label=\"PubMed Central reference 57\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 57\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Haplotype-resolved%20de%20novo%20assembly%20using%20phased%20assembly%20graphs%20with%20hifiasm&amp;journal=Nat.%20Methods&amp;doi=10.1038%2Fs41592-020-01056-5&amp;volume=18&amp;pages=170-175&amp;publication_year=2021&amp;author=Cheng%2CH&amp;author=Concepcion%2CGT&amp;author=Feng%2CX&amp;author=Zhang%2CH&amp;author=Li%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"58.\">\n<p class=\"c-article-references__text\" id=\"ref-CR58\">Guan, D. et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics <b>36<\/b>, 2896\u20132898 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btaa025\" data-track-item_id=\"10.1093\/bioinformatics\/btaa025\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtaa025\" aria-label=\"Article reference 58\" data-doi=\"10.1093\/bioinformatics\/btaa025\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXisFCktb%2FO\" aria-label=\"CAS reference 58\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31971576\" aria-label=\"PubMed reference 58\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7203741\" aria-label=\"PubMed Central reference 58\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 58\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Identifying%20and%20removing%20haplotypic%20duplication%20in%20primary%20genome%20assemblies.&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtaa025&amp;volume=36&amp;pages=2896-2898&amp;publication_year=2020&amp;author=Guan%2CD\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"59.\">\n<p class=\"c-article-references__text\" id=\"ref-CR59\">Zhao, X. &amp; Hao, W. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. <b>35<\/b>, W265\u2013W268 (2007).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkm286\" data-track-item_id=\"10.1093\/nar\/gkm286\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkm286\" aria-label=\"Article reference 59\" data-doi=\"10.1093\/nar\/gkm286\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 59\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=LTR_FINDER%3A%20an%20efficient%20tool%20for%20the%20prediction%20of%20full-length%20LTR%20retrotransposons&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkm286&amp;volume=35&amp;pages=W265-W268&amp;publication_year=2007&amp;author=Zhao%2CX&amp;author=Hao%2CW\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"60.\">\n<p class=\"c-article-references__text\" id=\"ref-CR60\">Ellinghaus, D., Kurtz, S. &amp; Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics <b>9<\/b>, 18 (2008).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/1471-2105-9-18\" data-track-item_id=\"10.1186\/1471-2105-9-18\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/1471-2105-9-18\" aria-label=\"Article reference 60\" data-doi=\"10.1186\/1471-2105-9-18\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=18194517\" aria-label=\"PubMed reference 60\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2253517\" aria-label=\"PubMed Central reference 60\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 60\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=LTRharvest%2C%20an%20efficient%20and%20flexible%20software%20for%20de%20novo%20detection%20of%20LTR%20retrotransposons.&amp;journal=BMC%20Bioinformatics&amp;doi=10.1186%2F1471-2105-9-18&amp;volume=9&amp;publication_year=2008&amp;author=Ellinghaus%2CD&amp;author=Kurtz%2CS&amp;author=Willhoeft%2CU\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"61.\">\n<p class=\"c-article-references__text\" id=\"ref-CR61\">Ou, S. &amp; Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol. <b>176<\/b>, 1410\u20131422 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1104\/pp.17.01310\" data-track-item_id=\"10.1104\/pp.17.01310\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1104%2Fpp.17.01310\" aria-label=\"Article reference 61\" data-doi=\"10.1104\/pp.17.01310\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1cXhs1CjtbzO\" aria-label=\"CAS reference 61\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=29233850\" aria-label=\"PubMed reference 61\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 61\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=LTR_retriever%3A%20a%20highly%20accurate%20and%20sensitive%20program%20for%20identification%20of%20long%20terminal%20repeat%20retrotransposons&amp;journal=Plant%20Physiol.&amp;doi=10.1104%2Fpp.17.01310&amp;volume=176&amp;pages=1410-1422&amp;publication_year=2018&amp;author=Ou%2CS&amp;author=Jiang%2CN\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"62.\">\n<p class=\"c-article-references__text\" id=\"ref-CR62\">Tarailo-Graovac, M. &amp; Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics <b>5<\/b>, 4.10.11\u201314.10.14 (2004).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 62\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Using%20RepeatMasker%20to%20identify%20repetitive%20elements%20in%20genomic%20sequences&amp;journal=Curr.%20Protoc.%20Bioinformatics&amp;volume=5&amp;pages=4.10.11-14.10.14&amp;publication_year=2004&amp;author=Tarailo-Graovac%2CM&amp;author=Chen%2CN\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"63.\">\n<p class=\"c-article-references__text\" id=\"ref-CR63\">Br\u016fna, T., Hoff, K. J., Lomsadze, A., Stanke, M. &amp; Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinform. <b>3<\/b>, lqaa108 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nargab\/lqaa108\" data-track-item_id=\"10.1093\/nargab\/lqaa108\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnargab%2Flqaa108\" aria-label=\"Article reference 63\" data-doi=\"10.1093\/nargab\/lqaa108\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33575650\" aria-label=\"PubMed reference 63\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7787252\" aria-label=\"PubMed Central reference 63\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 63\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=BRAKER2%3A%20automatic%20eukaryotic%20genome%20annotation%20with%20GeneMark-EP%2B%20and%20AUGUSTUS%20supported%20by%20a%20protein%20database&amp;journal=NAR%20Genom.%20Bioinform.&amp;doi=10.1093%2Fnargab%2Flqaa108&amp;volume=3&amp;publication_year=2021&amp;author=Br%C5%AFna%2CT&amp;author=Hoff%2CKJ&amp;author=Lomsadze%2CA&amp;author=Stanke%2CM&amp;author=Borodovsky%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"64.\">\n<p class=\"c-article-references__text\" id=\"ref-CR64\">Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. <b>34<\/b>, W435\u2013W439 (2006).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkl200\" data-track-item_id=\"10.1093\/nar\/gkl200\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkl200\" aria-label=\"Article reference 64\" data-doi=\"10.1093\/nar\/gkl200\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD28Xps1yiu78%3D\" aria-label=\"CAS reference 64\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=16845043\" aria-label=\"PubMed reference 64\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1538822\" aria-label=\"PubMed Central reference 64\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 64\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=AUGUSTUS%3A%20ab%20initio%20prediction%20of%20alternative%20transcripts&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkl200&amp;volume=34&amp;pages=W435-W439&amp;publication_year=2006&amp;author=Stanke%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"65.\">\n<p class=\"c-article-references__text\" id=\"ref-CR65\">Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics <b>30<\/b>, 1236\u20131240 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btu031\" data-track-item_id=\"10.1093\/bioinformatics\/btu031\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtu031\" aria-label=\"Article reference 65\" data-doi=\"10.1093\/bioinformatics\/btu031\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXmvFCjsr4%3D\" aria-label=\"CAS reference 65\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24451626\" aria-label=\"PubMed reference 65\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3998142\" aria-label=\"PubMed Central reference 65\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 65\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=InterProScan%205%3A%20genome-scale%20protein%20function%20classification&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtu031&amp;volume=30&amp;pages=1236-1240&amp;publication_year=2014&amp;author=Jones%2CP\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"66.\">\n<p class=\"c-article-references__text\" id=\"ref-CR66\">Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. <b>20<\/b>, 275 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/s13059-019-1905-y\" data-track-item_id=\"10.1186\/s13059-019-1905-y\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s13059-019-1905-y\" aria-label=\"Article reference 66\" data-doi=\"10.1186\/s13059-019-1905-y\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXisVSntb3O\" aria-label=\"CAS reference 66\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31843001\" aria-label=\"PubMed reference 66\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6913007\" aria-label=\"PubMed Central reference 66\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 66\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Benchmarking%20transposable%20element%20annotation%20methods%20for%20creation%20of%20a%20streamlined%2C%20comprehensive%20pipeline&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fs13059-019-1905-y&amp;volume=20&amp;publication_year=2019&amp;author=Ou%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"67.\">\n<p class=\"c-article-references__text\" id=\"ref-CR67\">Su, W., Gu, X. &amp; Peterson, T. TIR-Learner, a new ensemble method for TIR transposable element annotation, provides evidence for abundant new transposable elements in the maize genome. Mol. Plant <b>12<\/b>, 447\u2013460 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.molp.2019.02.008\" data-track-item_id=\"10.1016\/j.molp.2019.02.008\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.molp.2019.02.008\" aria-label=\"Article reference 67\" data-doi=\"10.1016\/j.molp.2019.02.008\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXjs1GgsLo%3D\" aria-label=\"CAS reference 67\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30802553\" aria-label=\"PubMed reference 67\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 67\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=TIR-Learner%2C%20a%20new%20ensemble%20method%20for%20TIR%20transposable%20element%20annotation%2C%20provides%20evidence%20for%20abundant%20new%20transposable%20elements%20in%20the%20maize%20genome&amp;journal=Mol.%20Plant&amp;doi=10.1016%2Fj.molp.2019.02.008&amp;volume=12&amp;pages=447-460&amp;publication_year=2019&amp;author=Su%2CW&amp;author=Gu%2CX&amp;author=Peterson%2CT\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"68.\">\n<p class=\"c-article-references__text\" id=\"ref-CR68\">Xiong, W. et al. HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes. Proc. Natl Acad. Sci. USA <b>111<\/b>, 10263\u201310268 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1073\/pnas.1410068111\" data-track-item_id=\"10.1073\/pnas.1410068111\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1073%2Fpnas.1410068111\" aria-label=\"Article reference 68\" data-doi=\"10.1073\/pnas.1410068111\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXhtVOitL7L\" aria-label=\"CAS reference 68\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24982153\" aria-label=\"PubMed reference 68\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4104883\" aria-label=\"PubMed Central reference 68\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 68\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=HelitronScanner%20uncovers%20a%20large%20overlooked%20cache%20of%20Helitron%20transposons%20in%20many%20plant%20genomes.&amp;journal=Proc.%20Natl%20Acad.%20Sci.%20USA&amp;doi=10.1073%2Fpnas.1410068111&amp;volume=111&amp;pages=10263-10268&amp;publication_year=2014&amp;author=Xiong%2CW\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"69.\">\n<p class=\"c-article-references__text\" id=\"ref-CR69\">Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA <b>117<\/b>, 9451\u20139457 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1073\/pnas.1921046117\" data-track-item_id=\"10.1073\/pnas.1921046117\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1073%2Fpnas.1921046117\" aria-label=\"Article reference 69\" data-doi=\"10.1073\/pnas.1921046117\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXnvFeqt74%3D\" aria-label=\"CAS reference 69\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32300014\" aria-label=\"PubMed reference 69\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7196820\" aria-label=\"PubMed Central reference 69\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 69\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=RepeatModeler2%20for%20automated%20genomic%20discovery%20of%20transposable%20element%20families&amp;journal=Proc.%20Natl%20Acad.%20Sci.%20USA&amp;doi=10.1073%2Fpnas.1921046117&amp;volume=117&amp;pages=9451-9457&amp;publication_year=2020&amp;author=Flynn%2CJM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"70.\">\n<p class=\"c-article-references__text\" id=\"ref-CR70\">Lavigne, R., Seto, D., Mahadevan, P., Ackermann, H.-W. &amp; Kropinski, A. M. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res. Microbiol. <b>159<\/b>, 406\u2013414 (2008).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.resmic.2008.03.005\" data-track-item_id=\"10.1016\/j.resmic.2008.03.005\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.resmic.2008.03.005\" aria-label=\"Article reference 70\" data-doi=\"10.1016\/j.resmic.2008.03.005\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1cXhtVSiu7%2FL\" aria-label=\"CAS reference 70\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=18555669\" aria-label=\"PubMed reference 70\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 70\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Unifying%20classical%20and%20molecular%20taxonomic%20classification%3A%20analysis%20of%20the%20Podoviridae%20using%20BLASTP-based%20tools&amp;journal=Res.%20Microbiol.&amp;doi=10.1016%2Fj.resmic.2008.03.005&amp;volume=159&amp;pages=406-414&amp;publication_year=2008&amp;author=Lavigne%2CR&amp;author=Seto%2CD&amp;author=Mahadevan%2CP&amp;author=Ackermann%2CH-W&amp;author=Kropinski%2CAM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"71.\">\n<p class=\"c-article-references__text\" id=\"ref-CR71\">Emms, D. M. &amp; Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. <b>20<\/b>, 238 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/s13059-019-1832-y\" data-track-item_id=\"10.1186\/s13059-019-1832-y\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s13059-019-1832-y\" aria-label=\"Article reference 71\" data-doi=\"10.1186\/s13059-019-1832-y\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31727128\" aria-label=\"PubMed reference 71\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6857279\" aria-label=\"PubMed Central reference 71\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 71\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=OrthoFinder%3A%20phylogenetic%20orthology%20inference%20for%20comparative%20genomics&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fs13059-019-1832-y&amp;volume=20&amp;publication_year=2019&amp;author=Emms%2CDM&amp;author=Kelly%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"72.\">\n<p class=\"c-article-references__text\" id=\"ref-CR72\">Wang, D., Zhang, Y., Zhang, Z., Zhu, J. &amp; Yu, J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics <b>8<\/b>, 77\u201380 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/S1672-0229(10)60008-3\" data-track-item_id=\"10.1016\/S1672-0229(10)60008-3\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2FS1672-0229%2810%2960008-3\" aria-label=\"Article reference 72\" data-doi=\"10.1016\/S1672-0229(10)60008-3\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3cXnsVOmurg%3D\" aria-label=\"CAS reference 72\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20451164\" aria-label=\"PubMed reference 72\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5054116\" aria-label=\"PubMed Central reference 72\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 72\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=KaKs_Calculator%202.0%3A%20a%20toolkit%20incorporating%20gamma-series%20methods%20and%20sliding%20window%20strategies&amp;journal=Genomics%20Proteomics%20Bioinformatics&amp;doi=10.1016%2FS1672-0229%2810%2960008-3&amp;volume=8&amp;pages=77-80&amp;publication_year=2010&amp;author=Wang%2CD&amp;author=Zhang%2CY&amp;author=Zhang%2CZ&amp;author=Zhu%2CJ&amp;author=Yu%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"73.\">\n<p class=\"c-article-references__text\" id=\"ref-CR73\">Wang, D.-P., Wan, H.-L., Zhang, S. &amp; Yu, J. \u03b3-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biol. Direct <b>4<\/b>, 20 (2009).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/1745-6150-4-20\" data-track-item_id=\"10.1186\/1745-6150-4-20\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/1745-6150-4-20\" aria-label=\"Article reference 73\" data-doi=\"10.1186\/1745-6150-4-20\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=19531225\" aria-label=\"PubMed reference 73\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2702329\" aria-label=\"PubMed Central reference 73\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 73\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=%CE%B3-MYN%3A%20a%20new%20algorithm%20for%20estimating%20Ka%20and%20Ks%20with%20consideration%20of%20variable%20substitution%20rates&amp;journal=Biol.%20Direct&amp;doi=10.1186%2F1745-6150-4-20&amp;volume=4&amp;publication_year=2009&amp;author=Wang%2CD-P&amp;author=Wan%2CH-L&amp;author=Zhang%2CS&amp;author=Yu%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"74.\">\n<p class=\"c-article-references__text\" id=\"ref-CR74\">Sedlazeck, F. J. et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods <b>15<\/b>, 461\u2013468 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41592-018-0001-7\" data-track-item_id=\"10.1038\/s41592-018-0001-7\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41592-018-0001-7\" aria-label=\"Article reference 74\" data-doi=\"10.1038\/s41592-018-0001-7\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1cXhtFOmtLrP\" aria-label=\"CAS reference 74\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=29713083\" aria-label=\"PubMed reference 74\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5990442\" aria-label=\"PubMed Central reference 74\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 74\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Accurate%20detection%20of%20complex%20structural%20variations%20using%20single-molecule%20sequencing&amp;journal=Nat.%20Methods&amp;doi=10.1038%2Fs41592-018-0001-7&amp;volume=15&amp;pages=461-468&amp;publication_year=2018&amp;author=Sedlazeck%2CFJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"75.\">\n<p class=\"c-article-references__text\" id=\"ref-CR75\">Heller, D. &amp; Vingron, M. SVIM: structural variant identification using mapped long reads. Bioinformatics <b>35<\/b>, 2907\u20132915 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btz041\" data-track-item_id=\"10.1093\/bioinformatics\/btz041\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtz041\" aria-label=\"Article reference 75\" data-doi=\"10.1093\/bioinformatics\/btz041\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhtValtrrM\" aria-label=\"CAS reference 75\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30668829\" aria-label=\"PubMed reference 75\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6735718\" aria-label=\"PubMed Central reference 75\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 75\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=SVIM%3A%20structural%20variant%20identification%20using%20mapped%20long%20reads&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtz041&amp;volume=35&amp;pages=2907-2915&amp;publication_year=2019&amp;author=Heller%2CD&amp;author=Vingron%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"76.\">\n<p class=\"c-article-references__text\" id=\"ref-CR76\">Jiang, T. et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. <b>21<\/b>, 189 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1186\/s13059-020-02107-y\" data-track-item_id=\"10.1186\/s13059-020-02107-y\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s13059-020-02107-y\" aria-label=\"Article reference 76\" data-doi=\"10.1186\/s13059-020-02107-y\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhsFegtrbO\" aria-label=\"CAS reference 76\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32746918\" aria-label=\"PubMed reference 76\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7477834\" aria-label=\"PubMed Central reference 76\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 76\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Long-read-based%20human%20genomic%20structural%20variation%20detection%20with%20cuteSV&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fs13059-020-02107-y&amp;volume=21&amp;publication_year=2020&amp;author=Jiang%2CT\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"77.\">\n<p class=\"c-article-references__text\" id=\"ref-CR77\">Jeffares, D. C. et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat. Commun. <b>8<\/b>, 14061 (2017).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/ncomms14061\" data-track-item_id=\"10.1038\/ncomms14061\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fncomms14061\" aria-label=\"Article reference 77\" data-doi=\"10.1038\/ncomms14061\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhsFejsLg%3D\" aria-label=\"CAS reference 77\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=28117401\" aria-label=\"PubMed reference 77\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5286201\" aria-label=\"PubMed Central reference 77\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 77\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Transient%20structural%20variations%20have%20strong%20effects%20on%20quantitative%20traits%20and%20reproductive%20isolation%20in%20fission%20yeast&amp;journal=Nat.%20Commun.&amp;doi=10.1038%2Fncomms14061&amp;volume=8&amp;publication_year=2017&amp;author=Jeffares%2CDC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"78.\">\n<p class=\"c-article-references__text\" id=\"ref-CR78\">Mar\u00e7ais, G. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. <b>14<\/b>, e1005944 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pcbi.1005944\" data-track-item_id=\"10.1371\/journal.pcbi.1005944\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pcbi.1005944\" aria-label=\"Article reference 78\" data-doi=\"10.1371\/journal.pcbi.1005944\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=29373581\" aria-label=\"PubMed reference 78\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5802927\" aria-label=\"PubMed Central reference 78\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 78\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=MUMmer4%3A%20a%20fast%20and%20versatile%20genome%20alignment%20system&amp;journal=PLoS%20Comput.%20Biol.&amp;doi=10.1371%2Fjournal.pcbi.1005944&amp;volume=14&amp;publication_year=2018&amp;author=Mar%C3%A7ais%2CG\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"79.\">\n<p class=\"c-article-references__text\" id=\"ref-CR79\">Quinlan, A. R. &amp; Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics <b>26<\/b>, 841\u2013842 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btq033\" data-track-item_id=\"10.1093\/bioinformatics\/btq033\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtq033\" aria-label=\"Article reference 79\" data-doi=\"10.1093\/bioinformatics\/btq033\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3cXivFGkurc%3D\" aria-label=\"CAS reference 79\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20110278\" aria-label=\"PubMed reference 79\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2832824\" aria-label=\"PubMed Central reference 79\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 79\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=BEDTools%3A%20a%20flexible%20suite%20of%20utilities%20for%20comparing%20genomic%20features&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtq033&amp;volume=26&amp;pages=841-842&amp;publication_year=2010&amp;author=Quinlan%2CAR&amp;author=Hall%2CIM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"80.\">\n<p class=\"c-article-references__text\" id=\"ref-CR80\">Zadeh, L. A. Fuzzy sets as a basis for a theory of possibility. Fuzzy Sets Syst. <b>1<\/b>, 3\u201328 (1978).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/0165-0114(78)90029-5\" data-track-item_id=\"10.1016\/0165-0114(78)90029-5\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2F0165-0114%2878%2990029-5\" aria-label=\"Article reference 80\" data-doi=\"10.1016\/0165-0114(78)90029-5\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 80\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Fuzzy%20sets%20as%20a%20basis%20for%20a%20theory%20of%20possibility&amp;journal=Fuzzy%20Sets%20Syst.&amp;doi=10.1016%2F0165-0114%2878%2990029-5&amp;volume=1&amp;pages=3-28&amp;publication_year=1978&amp;author=Zadeh%2CLA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"81.\">\n<p class=\"c-article-references__text\" id=\"ref-CR81\">VanRaden, P. M. Efficient methods to compute genomic predictions. J. Dairy Sci. <b>91<\/b>, 4414\u20134423 (2008).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.3168\/jds.2007-0980\" data-track-item_id=\"10.3168\/jds.2007-0980\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.3168%2Fjds.2007-0980\" aria-label=\"Article reference 81\" data-doi=\"10.3168\/jds.2007-0980\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1cXhtlajtLzO\" aria-label=\"CAS reference 81\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=18946147\" aria-label=\"PubMed reference 81\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 81\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Efficient%20methods%20to%20compute%20genomic%20predictions&amp;journal=J.%20Dairy%20Sci.&amp;doi=10.3168%2Fjds.2007-0980&amp;volume=91&amp;pages=4414-4423&amp;publication_year=2008&amp;author=VanRaden%2CPM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"82.\">\n<p class=\"c-article-references__text\" id=\"ref-CR82\">Cortes, C. &amp; Vapnik, V. Support-vector networks. Machine Leaning <b>20<\/b>, 273\u2013297 (1995).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1007\/BF00994018\" data-track-item_id=\"10.1007\/BF00994018\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/BF00994018\" aria-label=\"Article reference 82\" data-doi=\"10.1007\/BF00994018\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 82\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Support-vector%20networks.&amp;journal=Machine%20Leaning&amp;doi=10.1007%2FBF00994018&amp;volume=20&amp;pages=273-297&amp;publication_year=1995&amp;author=Cortes%2CC&amp;author=Vapnik%2CV\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"83.\">\n<p class=\"c-article-references__text\" id=\"ref-CR83\">Fu, C., Hernandez, T., Zhou, C. &amp; Wang, Z.-Y. Alfalfa (Medicago sativa L.). Methods Mol. Biol. <b>1223<\/b>, 213\u2013221 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener\" data-track-label=\"10.1007\/978-1-4939-1695-5_17\" data-track-item_id=\"10.1007\/978-1-4939-1695-5_17\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/978-1-4939-1695-5_17\" aria-label=\"Article reference 83\" data-doi=\"10.1007\/978-1-4939-1695-5_17\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28XjtVOrtLs%3D\" aria-label=\"CAS reference 83\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=25300843\" aria-label=\"PubMed reference 83\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 83\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Alfalfa%20%28Medicago%20sativa%20L.%29&amp;journal=Methods%20Mol.%20Biol.&amp;doi=10.1007%2F978-1-4939-1695-5_17&amp;volume=1223&amp;pages=213-221&amp;publication_year=2015&amp;author=Fu%2CC&amp;author=Hernandez%2CT&amp;author=Zhou%2CC&amp;author=Wang%2CZ-Y\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"84.\">\n<p class=\"c-article-references__text\" id=\"ref-CR84\">Abr\u00e0moff, M. D., Magalh\u00e3es, P. J. &amp; Ram, S. J. Image processing with ImageJ. Biophotonics Int. <b>11<\/b>, 36\u201342 (2004).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 84\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Image%20processing%20with%20ImageJ&amp;journal=Biophotonics%20Int.&amp;volume=11&amp;pages=36-42&amp;publication_year=2004&amp;author=Abr%C3%A0moff%2CMD&amp;author=Magalh%C3%A3es%2CPJ&amp;author=Ram%2CSJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"85.\">\n<p class=\"c-article-references__text\" id=\"ref-CR85\">He, F. Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa. Zenodo <a href=\"https:\/\/doi.org\/10.5281\/zenodo.14118212\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.5281\/zenodo.14118212\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.5281\/zenodo.14118212<\/a> (2024).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"86.\">\n<p class=\"c-article-references__text\" id=\"ref-CR86\">He, F. Alfalfa. Figshare <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.28426967.v1\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.6084\/m9.figshare.28426967.v1\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.6084\/m9.figshare.28426967.v1<\/a> (2025).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"87.\">\n<p class=\"c-article-references__text\" id=\"ref-CR87\">Fei, H. Alfalfa. Zenodo <a href=\"https:\/\/doi.org\/10.5281\/zenodo.14869062\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.5281\/zenodo.14869062\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.5281\/zenodo.14869062<\/a> (2025).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"88.\">\n<p class=\"c-article-references__text\" id=\"ref-CR88\">Fei, H. Alfalfa pan-genome. Zenodo <a href=\"https:\/\/doi.org\/10.5281\/zenodo.14800544\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.5281\/zenodo.14800544\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.5281\/zenodo.14800544<\/a> (2025).<\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Annicchiarico, P., Barrett, B., Brummer, E. C., Julier, B. &amp; Marshall, A. H. Achievements and challenges in improving&hellip;\n","protected":false},"author":2,"featured_media":43634,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3846],"tags":[3971,3973,3967,3970,3972,3968,267,3900,3969,24272,70,16,15],"class_list":{"0":"post-43633","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetics","8":"tag-agriculture","9":"tag-animal-genetics-and-genomics","10":"tag-biomedicine","11":"tag-cancer-research","12":"tag-gene-function","13":"tag-general","14":"tag-genetics","15":"tag-genomics","16":"tag-human-genetics","17":"tag-plant-breeding","18":"tag-science","19":"tag-uk","20":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/114386912416121841","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/43633","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/comments?post=43633"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/43633\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/43634"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=43633"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=43633"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=43633"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}