{"id":342974,"date":"2025-08-14T04:44:15","date_gmt":"2025-08-14T04:44:15","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/342974\/"},"modified":"2025-08-14T04:44:15","modified_gmt":"2025-08-14T04:44:15","slug":"the-genomic-origin-of-the-unique-chaetognath-body-plan","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/342974\/","title":{"rendered":"The genomic origin of the unique chaetognath body plan"},"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\">Erwin, D. H. The origin of animal body plans: a view from fossil evidence and the regulatory genome. Development <b>147<\/b>, dev182899 (2020).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXosVGgsb4%3D\" aria-label=\"CAS reference 1\" 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=32079678\" aria-label=\"PubMed reference 1\" 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 1\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20origin%20of%20animal%20body%20plans%3A%20a%20view%20from%20fossil%20evidence%20and%20the%20regulatory%20genome&amp;journal=Development&amp;volume=147&amp;publication_year=2020&amp;author=Erwin%2CDH\" 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\">Bone, Q., Kapp, H. &amp; Pierrot-Bults, A. C. The Biology of Chaetognaths (Oxford Univ. Press, 1991).<\/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\">Rieger, V. et al. Immunohistochemical analysis and 3D reconstruction of the cephalic nervous system in Chaetognatha: insights into the evolution of an early bilaterian brain? Invertebr. Biol. <b>129<\/b>, 77\u2013104 (2010).<\/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 3\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Immunohistochemical%20analysis%20and%203D%20reconstruction%20of%20the%20cephalic%20nervous%20system%20in%20Chaetognatha%3A%20insights%20into%20the%20evolution%20of%20an%20early%20bilaterian%20brain%3F&amp;journal=Invertebr.%20Biol.&amp;volume=129&amp;pages=77-104&amp;publication_year=2010&amp;author=Rieger%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=\"4.\">\n<p class=\"c-article-references__text\" id=\"ref-CR4\">M\u00fcller, C. H. G., Rieger, V., Perez, Y. &amp; Harzsch, S. Immunohistochemical and ultrastructural studies on ciliary sense organs of arrow worms (Chaetognatha). Zoomorphology <b>133<\/b>, 167\u2013189 (2014).<\/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 4\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Immunohistochemical%20and%20ultrastructural%20studies%20on%20ciliary%20sense%20organs%20of%20arrow%20worms%20%28Chaetognatha%29&amp;journal=Zoomorphology&amp;volume=133&amp;pages=167-189&amp;publication_year=2014&amp;author=M%C3%BCller%2CCHG&amp;author=Rieger%2CV&amp;author=Perez%2CY&amp;author=Harzsch%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=\"5.\">\n<p class=\"c-article-references__text\" id=\"ref-CR5\">Marl\u00e9taz, F., Peijnenburg, K. T. C. A., Goto, T., Satoh, N. &amp; Rokhsar, D. S. A new spiralian phylogeny places the enigmatic arrow worms among Gnathiferans. Curr. Biol. <b>29<\/b>, 312\u2013318.e3 (2019).<\/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=30639106\" aria-label=\"PubMed reference 5\" 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 5\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20new%20spiralian%20phylogeny%20places%20the%20enigmatic%20arrow%20worms%20among%20Gnathiferans&amp;journal=Curr.%20Biol.&amp;volume=29&amp;pages=312-318.e3&amp;publication_year=2019&amp;author=Marl%C3%A9taz%2CF&amp;author=Peijnenburg%2CKTCA&amp;author=Goto%2CT&amp;author=Satoh%2CN&amp;author=Rokhsar%2CDS\" 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\">Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. Biol. Sci. <b>286<\/b>, 20190831 (2019).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXit1ClsLnO\" aria-label=\"CAS reference 6\" 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=31288696\" 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\/PMC6650721\" 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=Revisiting%20metazoan%20phylogeny%20with%20genomic%20sampling%20of%20all%20phyla&amp;journal=Proc.%20Biol.%20Sci.&amp;volume=286&amp;publication_year=2019&amp;author=Laumer%2CCE\" 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\">Mart\u00edn-Zamora, F. M. et al. Annelid functional genomics reveal the origins of bilaterian life cycles. Nature <b>615<\/b>, 105\u2013110 (2023).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2023Natur.615..105M\" aria-label=\"ADS reference 7\" target=\"_blank\">ADS<\/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=36697830\" 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\/PMC9977687\" 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=Annelid%20functional%20genomics%20reveal%20the%20origins%20of%20bilaterian%20life%20cycles&amp;journal=Nature&amp;volume=615&amp;pages=105-110&amp;publication_year=2023&amp;author=Mart%C3%ADn-Zamora%2CFM\" 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\">Simakov, O. et al. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci. Adv. <b>8<\/b>, eabi5884 (2022).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2022SciA....8.5884S\" aria-label=\"ADS reference 8\" target=\"_blank\">ADS<\/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%2BB38XkvFyhu7Y%3D\" 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=35108053\" 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\/PMC8809688\" 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=Deeply%20conserved%20synteny%20and%20the%20evolution%20of%20metazoan%20chromosomes&amp;journal=Sci.%20Adv.&amp;volume=8&amp;publication_year=2022&amp;author=Simakov%2CO\" 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\">Telford, M. J. &amp; Holland, P. W. Evolution of 28S ribosomal DNA in chaetognaths: duplicate genes and molecular phylogeny. J. Mol. Evol. <b>44<\/b>, 135\u2013144 (1997).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=1997JMolE..44..135T\" aria-label=\"ADS reference 9\" target=\"_blank\">ADS<\/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:DyaK2sXhtFaksbw%3D\" aria-label=\"CAS reference 9\" 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=9069174\" 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=Evolution%20of%2028S%20ribosomal%20DNA%20in%20chaetognaths%3A%20duplicate%20genes%20and%20molecular%20phylogeny&amp;journal=J.%20Mol.%20Evol.&amp;volume=44&amp;pages=135-144&amp;publication_year=1997&amp;author=Telford%2CMJ&amp;author=Holland%2CPW\" 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\">Marl\u00e9taz, F. et al. Chaetognath transcriptome reveals ancestral and unique features among bilaterians. Genome Biol. <b>9<\/b>, R94 (2008).<\/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=18533022\" 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\/PMC2481426\" 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=Chaetognath%20transcriptome%20reveals%20ancestral%20and%20unique%20features%20among%20bilaterians&amp;journal=Genome%20Biol.&amp;volume=9&amp;publication_year=2008&amp;author=Marl%C3%A9taz%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=\"11.\">\n<p class=\"c-article-references__text\" id=\"ref-CR11\">Park, T.-Y. S. et al. A giant stem-group chaetognath. Sci. Adv. <b>10<\/b>, eadi6678 (2024).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXpvVyltg%3D%3D\" aria-label=\"CAS reference 11\" 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=38170772\" aria-label=\"PubMed reference 11\" 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\/PMC10796117\" aria-label=\"PubMed Central reference 11\" 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 11\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20giant%20stem-group%20chaetognath&amp;journal=Sci.%20Adv.&amp;volume=10&amp;publication_year=2024&amp;author=Park%2CT-YS\" 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\">Vinther, J. &amp; Parry, L. A. Bilateral jaw elements in Amiskwia sagittiformis bridge the morphological gap between Gnathiferans and Chaetognaths. Curr. Biol. <b>29<\/b>, 881\u2013888.e1 (2019).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXjs1GjtLo%3D\" 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=30799238\" 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=Bilateral%20jaw%20elements%20in%20Amiskwia%20sagittiformis%20bridge%20the%20morphological%20gap%20between%20Gnathiferans%20and%20Chaetognaths&amp;journal=Curr.%20Biol.&amp;volume=29&amp;pages=881-888.e1&amp;publication_year=2019&amp;author=Vinther%2CJ&amp;author=Parry%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=\"13.\">\n<p class=\"c-article-references__text\" id=\"ref-CR13\">Satoh, N. Chordate Origins and Evolution (Elsevier, 2016).<\/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\">Budd, G. E. &amp; Telford, M. J. The origin and evolution of arthropods. Nature <b>457<\/b>, 812\u2013817 (2009).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2009Natur.457..812B\" aria-label=\"ADS reference 14\" target=\"_blank\">ADS<\/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%2BD1MXhslCnsLo%3D\" aria-label=\"CAS reference 14\" 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=19212398\" 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=The%20origin%20and%20evolution%20of%20arthropods&amp;journal=Nature&amp;volume=457&amp;pages=812-817&amp;publication_year=2009&amp;author=Budd%2CGE&amp;author=Telford%2CMJ\" 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\">Chen, H. et al. A Cambrian crown annelid reconciles phylogenomics and the fossil record. Nature <b>583<\/b>, 249\u2013252 (2020).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2020Natur.583..249C\" aria-label=\"ADS reference 15\" target=\"_blank\">ADS<\/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%2BB3cXhtFCnurvL\" aria-label=\"CAS reference 15\" 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=32528177\" aria-label=\"PubMed reference 15\" 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 15\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20Cambrian%20crown%20annelid%20reconciles%20phylogenomics%20and%20the%20fossil%20record&amp;journal=Nature&amp;volume=583&amp;pages=249-252&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=\"16.\">\n<p class=\"c-article-references__text\" id=\"ref-CR16\">John, C. C. Memoirs: habits, structure, and development of Spadella cephaloptera. Q. J. Microsc. Sci. <b>75<\/b>, 625\u2013696 (1933).<\/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 16\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Memoirs%3A%20habits%2C%20structure%2C%20and%20development%20of%20Spadella%20cephaloptera&amp;journal=Q.%20J.%20Microsc.%20Sci.&amp;volume=75&amp;pages=625-696&amp;publication_year=1933&amp;author=John%2CCC\" 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\">Telford, M. J. &amp; Holland, P. W. The phylogenetic affinities of the chaetognaths: a molecular analysis. Mol. Biol. Evol. <b>10<\/b>, 660\u2013676 (1993).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DyaK3sXks1ymsLc%3D\" 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=8336548\" aria-label=\"PubMed reference 17\" 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 17\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20phylogenetic%20affinities%20of%20the%20chaetognaths%3A%20a%20molecular%20analysis&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=10&amp;pages=660-676&amp;publication_year=1993&amp;author=Telford%2CMJ&amp;author=Holland%2CPW\" 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\">Fr\u00f6bius, A. C. &amp; Funch, P. Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans. Nat. Commun. <b>8<\/b>, 9 (2017).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2017NatCo...8....9F\" aria-label=\"ADS reference 18\" target=\"_blank\">ADS<\/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=28377584\" aria-label=\"PubMed reference 18\" 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\/PMC5431905\" aria-label=\"PubMed Central reference 18\" 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 18\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Rotiferan%20Hox%20genes%20give%20new%20insights%20into%20the%20evolution%20of%20metazoan%20bodyplans&amp;journal=Nat.%20Commun.&amp;volume=8&amp;publication_year=2017&amp;author=Fr%C3%B6bius%2CAC&amp;author=Funch%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=\"19.\">\n<p class=\"c-article-references__text\" id=\"ref-CR19\">Papillon, D., Perez, Y., Fasano, L., Le Parco, Y. &amp; Caubit, X. Hox gene survey in the chaetognath Spadella cephaloptera: evolutionary implications. Dev. Genes Evol. <b>213<\/b>, 142\u2013148 (2003).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD3sXislyqt7g%3D\" aria-label=\"CAS reference 19\" 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=12690453\" aria-label=\"PubMed reference 19\" 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 19\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Hox%20gene%20survey%20in%20the%20chaetognath%20Spadella%20cephaloptera%3A%20evolutionary%20implications&amp;journal=Dev.%20Genes%20Evol.&amp;volume=213&amp;pages=142-148&amp;publication_year=2003&amp;author=Papillon%2CD&amp;author=Perez%2CY&amp;author=Fasano%2CL&amp;author=Parco%2CY&amp;author=Caubit%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=\"20.\">\n<p class=\"c-article-references__text\" id=\"ref-CR20\">Bekkouche, N. &amp; G\u0105siorowski, L. Careful amendment of morphological data sets improves phylogenetic frameworks: re-evaluating placement of the fossil Amiskwia sagittiformis. J. Syst. Palaeontol. <b>20<\/b>, 1\u201314 (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 20\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Careful%20amendment%20of%20morphological%20data%20sets%20improves%20phylogenetic%20frameworks%3A%20re-evaluating%20placement%20of%20the%20fossil%20Amiskwia%20sagittiformis&amp;journal=J.%20Syst.%20Palaeontol.&amp;volume=20&amp;pages=1-14&amp;publication_year=2022&amp;author=Bekkouche%2CN&amp;author=G%C4%85siorowski%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=\"21.\">\n<p class=\"c-article-references__text\" id=\"ref-CR21\">Marl\u00e9taz, F. et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature <b>564<\/b>, 64\u201370 (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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2018Natur.564...64M\" aria-label=\"ADS reference 21\" target=\"_blank\">ADS<\/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=30464347\" 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\/PMC6292497\" 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=Amphioxus%20functional%20genomics%20and%20the%20origins%20of%20vertebrate%20gene%20regulation&amp;journal=Nature&amp;volume=564&amp;pages=64-70&amp;publication_year=2018&amp;author=Marl%C3%A9taz%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=\"22.\">\n<p class=\"c-article-references__text\" id=\"ref-CR22\">Parey, E. et al. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat. Ecol. Evol. <b>8<\/b>, 1505\u20131521 (2024).<\/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=39030276\" aria-label=\"PubMed reference 22\" 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\/PMC11310086\" aria-label=\"PubMed Central reference 22\" 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 22\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20brittle%20star%20genome%20illuminates%20the%20genetic%20basis%20of%20animal%20appendage%20regeneration&amp;journal=Nat.%20Ecol.%20Evol.&amp;volume=8&amp;pages=1505-1521&amp;publication_year=2024&amp;author=Parey%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=\"23.\">\n<p class=\"c-article-references__text\" id=\"ref-CR23\">Simakov, O. et al. Insights into bilaterian evolution from three spiralian genomes. Nature <b>493<\/b>, 526\u2013531 (2013).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2013Natur.493..526S\" aria-label=\"ADS reference 23\" target=\"_blank\">ADS<\/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%2BC38XhvV2ntLjN\" 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=23254933\" aria-label=\"PubMed reference 23\" 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 23\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Insights%20into%20bilaterian%20evolution%20from%20three%20spiralian%20genomes&amp;journal=Nature&amp;volume=493&amp;pages=526-531&amp;publication_year=2013&amp;author=Simakov%2CO\" 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\">Luo, Y.-J. et al. The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization. Nat. Commun. <b>6<\/b>, 8301 (2015).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2015NatCo...6.8301L\" aria-label=\"ADS reference 24\" target=\"_blank\">ADS<\/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%2BC2MXhsFeisLvI\" 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=26383154\" 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=The%20Lingula%20genome%20provides%20insights%20into%20brachiopod%20evolution%20and%20the%20origin%20of%20phosphate%20biomineralization&amp;journal=Nat.%20Commun.&amp;volume=6&amp;publication_year=2015&amp;author=Luo%2CY-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=\"25.\">\n<p class=\"c-article-references__text\" id=\"ref-CR25\">Simion, P. et al. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Sci. Adv. <b>7<\/b>, eabg4216 (2021).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2021SciA....7.4216S\" aria-label=\"ADS reference 25\" target=\"_blank\">ADS<\/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%2BB3MXisFCisrjF\" 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=34613768\" aria-label=\"PubMed reference 25\" 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\/PMC8494291\" aria-label=\"PubMed Central reference 25\" 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 25\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Chromosome-level%20genome%20assembly%20reveals%20homologous%20chromosomes%20and%20recombination%20in%20asexual%20rotifer%20Adineta%20vaga&amp;journal=Sci.%20Adv.&amp;volume=7&amp;publication_year=2021&amp;author=Simion%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=\"26.\">\n<p class=\"c-article-references__text\" id=\"ref-CR26\">Flot, J.-F. et al. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature <b>500<\/b>, 453\u2013457 (2013).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2013Natur.500..453F\" aria-label=\"ADS reference 26\" target=\"_blank\">ADS<\/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%2BC3sXhtFCku7zL\" aria-label=\"CAS reference 26\" 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=23873043\" aria-label=\"PubMed reference 26\" 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 26\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Genomic%20evidence%20for%20ameiotic%20evolution%20in%20the%20bdelloid%20rotifer%20Adineta%20vaga&amp;journal=Nature&amp;volume=500&amp;pages=453-457&amp;publication_year=2013&amp;author=Flot%2CJ-F\" 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\">Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. <b>17<\/b>, 744\u2013757 (2016).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28XhvVShsr3J\" aria-label=\"CAS reference 27\" 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=27818507\" aria-label=\"PubMed reference 27\" 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 27\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20origin%20and%20evolution%20of%20cell%20types&amp;journal=Nat.%20Rev.%20Genet.&amp;volume=17&amp;pages=744-757&amp;publication_year=2016&amp;author=Arendt%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=\"28.\">\n<p class=\"c-article-references__text\" id=\"ref-CR28\">Goto, T. &amp; Yoshida, M. The mating sequence of the benthic arrowworm Spadella schizoptera. Biol. Bull. <b>169<\/b>, 328\u2013333 (1985).<\/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=29314916\" aria-label=\"PubMed reference 28\" 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 28\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20mating%20sequence%20of%20the%20benthic%20arrowworm%20Spadella%20schizoptera&amp;journal=Biol.%20Bull.&amp;volume=169&amp;pages=328-333&amp;publication_year=1985&amp;author=Goto%2CT&amp;author=Yoshida%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=\"29.\">\n<p class=\"c-article-references__text\" id=\"ref-CR29\">Ren-feng, W. Analysis of chromosome karyotypes in Chaetognath Sagitta crassa. J. Dalian Fish. Univ. <b>26<\/b>, 260\u2013263 (2011).<\/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%20chromosome%20karyotypes%20in%20Chaetognath%20Sagitta%20crassa&amp;journal=J.%20Dalian%20Fish.%20Univ.&amp;volume=26&amp;pages=260-263&amp;publication_year=2011&amp;author=Ren-feng%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=\"30.\">\n<p class=\"c-article-references__text\" id=\"ref-CR30\">Lewin, T. D. et al. Fusion, fission, and scrambling of the bilaterian genome in Bryozoa. Genome Res. <b>35<\/b>, 78\u201392 (2025).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXjtFGmsrc%3D\" 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=39762050\" 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\/PMC11789643\" 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=Fusion%2C%20fission%2C%20and%20scrambling%20of%20the%20bilaterian%20genome%20in%20Bryozoa&amp;journal=Genome%20Res.&amp;volume=35&amp;pages=78-92&amp;publication_year=2025&amp;author=Lewin%2CTD\" 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\">Guijarro-Clarke, C., Holland, P. W. H. &amp; Paps, J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat. Ecol. Evol. <b>4<\/b>, 519\u2013523 (2020).<\/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=32094540\" 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=Widespread%20patterns%20of%20gene%20loss%20in%20the%20evolution%20of%20the%20animal%20kingdom&amp;journal=Nat.%20Ecol.%20Evol.&amp;volume=4&amp;pages=519-523&amp;publication_year=2020&amp;author=Guijarro-Clarke%2CC&amp;author=Holland%2CPWH&amp;author=Paps%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=\"32.\">\n<p class=\"c-article-references__text\" id=\"ref-CR32\">Senaratne, A. P. et al. Formation of the CenH3-deficient holocentromere in Lepidoptera avoids active chromatin. Curr. Biol. <b>31<\/b>, 173\u2013181.e7 (2021).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXit1Gru7%2FF\" 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=33125865\" 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=Formation%20of%20the%20CenH3-deficient%20holocentromere%20in%20Lepidoptera%20avoids%20active%20chromatin&amp;journal=Curr.%20Biol.&amp;volume=31&amp;pages=173-181.e7&amp;publication_year=2021&amp;author=Senaratne%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=\"33.\">\n<p class=\"c-article-references__text\" id=\"ref-CR33\">Hofstatter, P. G. et al. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell <b>185<\/b>, 3153\u20133168.e18 (2022).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38XitVegsr3N\" 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=35926507\" aria-label=\"PubMed reference 33\" 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 33\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Repeat-based%20holocentromeres%20influence%20genome%20architecture%20and%20karyotype%20evolution&amp;journal=Cell&amp;volume=185&amp;pages=3153-3168.e18&amp;publication_year=2022&amp;author=Hofstatter%2CPG\" 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\">Lewin, T. D., Liao, I. J.-Y. &amp; Luo, Y.-J. Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians. Mol. Biol. Evol. <b>41<\/b>, msae172 (2024).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXivVSmsr7I\" 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=39141777\" aria-label=\"PubMed reference 34\" 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\/PMC11371463\" aria-label=\"PubMed Central reference 34\" 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 34\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Annelid%20comparative%20genomics%20and%20the%20evolution%20of%20massive%20lineage-specific%20genome%20rearrangement%20in%20bilaterians&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=41&amp;publication_year=2024&amp;author=Lewin%2CTD&amp;author=Liao%2CIJ-Y&amp;author=Luo%2CY-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=\"35.\">\n<p class=\"c-article-references__text\" id=\"ref-CR35\">Muller, H., Gil, J. Jr &amp; Drinnenberg, I. A. The impact of centromeres on spatial genome architecture. Trends Genet. <b>35<\/b>, 565\u2013578 (2019).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhtVegtbvF\" 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=31200946\" aria-label=\"PubMed reference 35\" 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 35\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20impact%20of%20centromeres%20on%20spatial%20genome%20architecture&amp;journal=Trends%20Genet.&amp;volume=35&amp;pages=565-578&amp;publication_year=2019&amp;author=Muller%2CH&amp;author=Gil%2CJ&amp;author=Drinnenberg%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=\"36.\">\n<p class=\"c-article-references__text\" id=\"ref-CR36\">Houtain, A. et al. Transgenerational chromosome repair in the asexual bdelloid rotifer Adineta vaga. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2024.01.25.577190\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2024.01.25.577190\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.1101\/2024.01.25.577190<\/a> (2024).<\/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\">Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science <b>326<\/b>, 289\u2013293 (2009).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2009Sci...326..289L\" aria-label=\"ADS reference 37\" target=\"_blank\">ADS<\/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%2BD1MXht1agsbjM\" 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=19815776\" aria-label=\"PubMed reference 37\" 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\/PMC2858594\" aria-label=\"PubMed Central reference 37\" 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 37\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Comprehensive%20mapping%20of%20long-range%20interactions%20reveals%20folding%20principles%20of%20the%20human%20genome&amp;journal=Science&amp;volume=326&amp;pages=289-293&amp;publication_year=2009&amp;author=Lieberman-Aiden%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=\"38.\">\n<p class=\"c-article-references__text\" id=\"ref-CR38\">\u00c1lvarez-Campos, P. et al. Annelid adult cell type diversity and their pluripotent cellular origins. Nat. Commun. <b>15<\/b>, 3194 (2024).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2024NatCo..15.3194A\" aria-label=\"ADS reference 38\" target=\"_blank\">ADS<\/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=38609365\" aria-label=\"PubMed reference 38\" 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\/PMC11014941\" aria-label=\"PubMed Central reference 38\" 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 38\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Annelid%20adult%20cell%20type%20diversity%20and%20their%20pluripotent%20cellular%20origins&amp;journal=Nat.%20Commun.&amp;volume=15&amp;publication_year=2024&amp;author=%C3%81lvarez-Campos%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=\"39.\">\n<p class=\"c-article-references__text\" id=\"ref-CR39\">Piovani, L. et al. Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories. Sci. Adv. <b>9<\/b>, eadg6034 (2023).<\/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=\"mathscinet reference\" data-track-action=\"mathscinet reference\" href=\"http:\/\/www.ams.org\/mathscinet-getitem?mr=4629506\" aria-label=\"MathSciNet reference 39\" target=\"_blank\">MathSciNet<\/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%2BB3sXhs1Gmur3F\" 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=37531419\" 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\/PMC10396302\" 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=Single-cell%20atlases%20of%20two%20lophotrochozoan%20larvae%20highlight%20their%20complex%20evolutionary%20histories&amp;journal=Sci.%20Adv.&amp;volume=9&amp;publication_year=2023&amp;author=Piovani%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=\"40.\">\n<p class=\"c-article-references__text\" id=\"ref-CR40\">Li, J. et al. Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types. Nat. Genet. <b>54<\/b>, 1711\u20131720 (2022).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38Xis1eitbjP\" 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=36229673\" aria-label=\"PubMed reference 40\" 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 40\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Deep%20learning%20of%20cross-species%20single-cell%20landscapes%20identifies%20conserved%20regulatory%20programs%20underlying%20cell%20types&amp;journal=Nat.%20Genet.&amp;volume=54&amp;pages=1711-1720&amp;publication_year=2022&amp;author=Li%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=\"41.\">\n<p class=\"c-article-references__text\" id=\"ref-CR41\">Rieger, V. et al. Development of the nervous system in hatchlings of Spadella cephaloptera (Chaetognatha), and implications for nervous system evolution in Bilateria. Dev. Growth Differ. <b>53<\/b>, 740\u2013759 (2011).<\/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=21671921\" 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=Development%20of%20the%20nervous%20system%20in%20hatchlings%20of%20Spadella%20cephaloptera%20%28Chaetognatha%29%2C%20and%20implications%20for%20nervous%20system%20evolution%20in%20Bilateria&amp;journal=Dev.%20Growth%20Differ.&amp;volume=53&amp;pages=740-759&amp;publication_year=2011&amp;author=Rieger%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=\"42.\">\n<p class=\"c-article-references__text\" id=\"ref-CR42\">Wollesen, T., Rodriguez Monje, S. V., Oel, A. P. &amp; Arendt, D. Characterization of eyes, photoreceptors, and opsins in developmental stages of the arrow worm Spadella cephaloptera (Chaetognatha). J. Exp. Zool. B <b>340<\/b>, 342\u2013353 (2023).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXkvFOitrg%3D\" aria-label=\"CAS reference 42\" 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 42\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Characterization%20of%20eyes%2C%20photoreceptors%2C%20and%20opsins%20in%20developmental%20stages%20of%20the%20arrow%20worm%20Spadella%20cephaloptera%20%28Chaetognatha%29&amp;journal=J.%20Exp.%20Zool.%20B&amp;volume=340&amp;pages=342-353&amp;publication_year=2023&amp;author=Wollesen%2CT&amp;author=Rodriguez%20Monje%2CSV&amp;author=Oel%2CAP&amp;author=Arendt%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=\"43.\">\n<p class=\"c-article-references__text\" id=\"ref-CR43\">Wu, L. et al. Genes with spiralian-specific protein motifs are expressed in spiralian ciliary bands. Nat. Commun. <b>11<\/b>, 4171 (2020).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2020NatCo..11.4171W\" aria-label=\"ADS reference 43\" target=\"_blank\">ADS<\/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%2BB3cXhs1Kltb%2FI\" aria-label=\"CAS reference 43\" 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=32820176\" aria-label=\"PubMed reference 43\" 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\/PMC7441323\" aria-label=\"PubMed Central reference 43\" 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 43\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Genes%20with%20spiralian-specific%20protein%20motifs%20are%20expressed%20in%20spiralian%20ciliary%20bands&amp;journal=Nat.%20Commun.&amp;volume=11&amp;publication_year=2020&amp;author=Wu%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\">Yasuda, E., Goto, T., Makabe, K. W. &amp; Satoh, N. Expression of actin genes in the arrow worm Paraspadella gotoi (Chaetognatha). Zoolog. Sci. <b>14<\/b>, 953\u2013960 (1997).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DyaK1cXitFelsbs%3D\" aria-label=\"CAS reference 44\" 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=9520638\" aria-label=\"PubMed reference 44\" 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 44\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Expression%20of%20actin%20genes%20in%20the%20arrow%20worm%20Paraspadella%20gotoi%20%28Chaetognatha%29&amp;journal=Zoolog.%20Sci.&amp;volume=14&amp;pages=953-960&amp;publication_year=1997&amp;author=Yasuda%2CE&amp;author=Goto%2CT&amp;author=Makabe%2CKW&amp;author=Satoh%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=\"45.\">\n<p class=\"c-article-references__text\" id=\"ref-CR45\">Carr\u00e9, D., Djediat, C. &amp; Sardet, C. Formation of a large Vasa-positive germ granule and its inheritance by germ cells in the enigmatic Chaetognaths. Development <b>129<\/b>, 661\u2013670 (2002).<\/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=11830567\" 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=Formation%20of%20a%20large%20Vasa-positive%20germ%20granule%20and%20its%20inheritance%20by%20germ%20cells%20in%20the%20enigmatic%20Chaetognaths&amp;journal=Development&amp;volume=129&amp;pages=661-670&amp;publication_year=2002&amp;author=Carr%C3%A9%2CD&amp;author=Djediat%2CC&amp;author=Sardet%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=\"46.\">\n<p class=\"c-article-references__text\" id=\"ref-CR46\">Piovani, L. &amp; Marl\u00e9taz, F. Single-cell transcriptomics refuels the exploration of spiralian biology. Brief. Funct. Genomics <b>22<\/b>, 517\u2013524 (2023).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXhsVCis7zK\" 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=37609674\" 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\/PMC10658179\" 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=Single-cell%20transcriptomics%20refuels%20the%20exploration%20of%20spiralian%20biology&amp;journal=Brief.%20Funct.%20Genomics&amp;volume=22&amp;pages=517-524&amp;publication_year=2023&amp;author=Piovani%2CL&amp;author=Marl%C3%A9taz%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=\"47.\">\n<p class=\"c-article-references__text\" id=\"ref-CR47\">Seb\u00e9-Pedr\u00f3s, A. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. <b>2<\/b>, 1176\u20131188 (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=29942020\" 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\/PMC6040636\" 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=Early%20metazoan%20cell%20type%20diversity%20and%20the%20evolution%20of%20multicellular%20gene%20regulation&amp;journal=Nat.%20Ecol.%20Evol.&amp;volume=2&amp;pages=1176-1188&amp;publication_year=2018&amp;author=Seb%C3%A9-Pedr%C3%B3s%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=\"48.\">\n<p class=\"c-article-references__text\" id=\"ref-CR48\">Goto, T. &amp; Yoshida, M. in Nervous Systems in Invertebrates (ed. Ali, M. A.) 461\u2013481 (Springer, 1987).<\/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\">Ahnelt, P. Chaetognatha. in Biology of the Integument: Invertebrates (eds. Bereiter-Hahn, J., Matoltsy, A. G. &amp; Richards, K. S.) 746\u2013755 (Springer, 1984).<\/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\">Valencia-Montoya, W. A., Pierce, N. E. &amp; Bellono, N. W. Evolution of sensory receptors. Annu. Rev. Cell Dev. Biol. <b>40<\/b>, 353\u2013379 (2024).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXitFGqtr3O\" aria-label=\"CAS reference 50\" 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=38985841\" 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\/PMC11526382\" 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=Evolution%20of%20sensory%20receptors&amp;journal=Annu.%20Rev.%20Cell%20Dev.%20Biol.&amp;volume=40&amp;pages=353-379&amp;publication_year=2024&amp;author=Valencia-Montoya%2CWA&amp;author=Pierce%2CNE&amp;author=Bellono%2CNW\" 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\">Vakirlis, N., Carvunis, A.-R. &amp; McLysaght, A. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife <b>9<\/b>, e53500 (2020).<\/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=32066524\" 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\/PMC7028367\" 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=Synteny-based%20analyses%20indicate%20that%20sequence%20divergence%20is%20not%20the%20main%20source%20of%20orphan%20genes&amp;journal=eLife&amp;volume=9&amp;publication_year=2020&amp;author=Vakirlis%2CN&amp;author=Carvunis%2CA-R&amp;author=McLysaght%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=\"52.\">\n<p class=\"c-article-references__text\" id=\"ref-CR52\">Maeso, I., Acemel, R. D. &amp; G\u00f3mez-Skarmeta, J. L. Cis-regulatory landscapes in development and evolution. Curr. Opin. Genet. Dev. <b>43<\/b>, 17\u201322 (2017).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28XhslelsL%2FF\" 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=27842294\" 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=Cis-regulatory%20landscapes%20in%20development%20and%20evolution&amp;journal=Curr.%20Opin.%20Genet.%20Dev.&amp;volume=43&amp;pages=17-22&amp;publication_year=2017&amp;author=Maeso%2CI&amp;author=Acemel%2CRD&amp;author=G%C3%B3mez-Skarmeta%2CJL\" 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\">de Mendoza, A. et al. Convergent evolution of a vertebrate-like methylome in a marine sponge. Nat. Ecol. Evol. <b>3<\/b>, 1464\u20131473 (2019).<\/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=31558833\" aria-label=\"PubMed reference 53\" 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\/PMC6783312\" aria-label=\"PubMed Central reference 53\" 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 53\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Convergent%20evolution%20of%20a%20vertebrate-like%20methylome%20in%20a%20marine%20sponge&amp;journal=Nat.%20Ecol.%20Evol.&amp;volume=3&amp;pages=1464-1473&amp;publication_year=2019&amp;author=Mendoza%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=\"54.\">\n<p class=\"c-article-references__text\" id=\"ref-CR54\">Ro\u0161i\u0107, S. et al. Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity. Nat. Genet. <b>50<\/b>, 452\u2013459 (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=29459678\" aria-label=\"PubMed reference 54\" 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\/PMC5865749\" aria-label=\"PubMed Central reference 54\" 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 54\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Evolutionary%20analysis%20indicates%20that%20DNA%20alkylation%20damage%20is%20a%20byproduct%20of%20cytosine%20DNA%20methyltransferase%20activity&amp;journal=Nat.%20Genet.&amp;volume=50&amp;pages=452-459&amp;publication_year=2018&amp;author=Ro%C5%A1i%C4%87%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=\"55.\">\n<p class=\"c-article-references__text\" id=\"ref-CR55\">Kim, I. V. et al. Chromatin loops are an ancestral hallmark of the animal regulatory genome. Nature <b>642<\/b>, 1097\u20131105 (2025).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXhsFCgs73O\" aria-label=\"CAS reference 55\" 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=40335694\" 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\/PMC12221973\" 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=Chromatin%20loops%20are%20an%20ancestral%20hallmark%20of%20the%20animal%20regulatory%20genome&amp;journal=Nature&amp;volume=642&amp;pages=1097-1105&amp;publication_year=2025&amp;author=Kim%2CIV\" 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\">Guynes, K. et al. Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria. Genome Biol. <b>25<\/b>, 204 (2024)<\/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\">Schwaiger, M. et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. <b>24<\/b>, 639\u2013650 (2014).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXmt1CrsL4%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=24642862\" 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\/PMC3975063\" 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=Evolutionary%20conservation%20of%20the%20eumetazoan%20gene%20regulatory%20landscape&amp;journal=Genome%20Res.&amp;volume=24&amp;pages=639-650&amp;publication_year=2014&amp;author=Schwaiger%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=\"58.\">\n<p class=\"c-article-references__text\" id=\"ref-CR58\">Barau, J. et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science <b>354<\/b>, 909\u2013912 (2016).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2016Sci...354..909B\" aria-label=\"ADS reference 58\" target=\"_blank\">ADS<\/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%2BC28XhvFGrtb%2FJ\" 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=27856912\" aria-label=\"PubMed reference 58\" 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 58\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20DNA%20methyltransferase%20DNMT3C%20protects%20male%20germ%20cells%20from%20transposon%20activity&amp;journal=Science&amp;volume=354&amp;pages=909-912&amp;publication_year=2016&amp;author=Barau%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=\"59.\">\n<p class=\"c-article-references__text\" id=\"ref-CR59\">Zaslaver, A., Baugh, L. R. &amp; Sternberg, P. W. Metazoan operons accelerate recovery from growth-arrested states. Cell <b>145<\/b>, 981\u2013992 (2011).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3MXnsVOkt7c%3D\" aria-label=\"CAS reference 59\" 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=21663799\" aria-label=\"PubMed reference 59\" 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\/PMC3152313\" aria-label=\"PubMed Central reference 59\" 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 59\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Metazoan%20operons%20accelerate%20recovery%20from%20growth-arrested%20states&amp;journal=Cell&amp;volume=145&amp;pages=981-992&amp;publication_year=2011&amp;author=Zaslaver%2CA&amp;author=Baugh%2CLR&amp;author=Sternberg%2CPW\" 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\">Douris, V., Telford, M. J. &amp; Averof, M. Evidence for multiple independent origins of trans-splicing in Metazoa. Mol. Biol. Evol. <b>27<\/b>, 684\u2013693 (2010).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3cXitlarsL0%3D\" aria-label=\"CAS reference 60\" 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=19942614\" aria-label=\"PubMed reference 60\" 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 60\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Evidence%20for%20multiple%20independent%20origins%20of%20trans-splicing%20in%20Metazoa&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=27&amp;pages=684-693&amp;publication_year=2010&amp;author=Douris%2CV&amp;author=Telford%2CMJ&amp;author=Averof%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=\"61.\">\n<p class=\"c-article-references__text\" id=\"ref-CR61\">Danks, G. B. et al. Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest. Mol. Biol. Evol. <b>32<\/b>, 585\u2013599 (2015).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28Xht1Oqt7%2FP\" 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=25525214\" 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=Trans-splicing%20and%20operons%20in%20metazoans%3A%20translational%20control%20in%20maternally%20regulated%20development%20and%20recovery%20from%20growth%20arrest&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=32&amp;pages=585-599&amp;publication_year=2015&amp;author=Danks%2CGB\" 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\">Wilson, C. G., Pieszko, T., Nowell, R. W. &amp; Barraclough, T. G. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet. <b>40<\/b>, 422\u2013436 (2024).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXlsVOhsro%3D\" aria-label=\"CAS reference 62\" 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=38458877\" aria-label=\"PubMed reference 62\" 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 62\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Recombination%20in%20bdelloid%20rotifer%20genomes%3A%20asexuality%2C%20transfer%20and%20stress&amp;journal=Trends%20Genet.&amp;volume=40&amp;pages=422-436&amp;publication_year=2024&amp;author=Wilson%2CCG&amp;author=Pieszko%2CT&amp;author=Nowell%2CRW&amp;author=Barraclough%2CTG\" 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\">Morel, B., Kozlov, A. M., Stamatakis, A. &amp; Sz\u00f6ll\u0151si, G. J. GeneRax: a tool for species-tree-aware maximum likelihood-based gene family tree inference under gene duplication, transfer, and loss. Mol. Biol. Evol. <b>37<\/b>, 2763\u20132774 (2020).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXis1egtbfI\" aria-label=\"CAS reference 63\" 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=32502238\" 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\/PMC8312565\" 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=GeneRax%3A%20a%20tool%20for%20species-tree-aware%20maximum%20likelihood-based%20gene%20family%20tree%20inference%20under%20gene%20duplication%2C%20transfer%2C%20and%20loss&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=37&amp;pages=2763-2774&amp;publication_year=2020&amp;author=Morel%2CB&amp;author=Kozlov%2CAM&amp;author=Stamatakis%2CA&amp;author=Sz%C3%B6ll%C5%91si%2CGJ\" 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\">Goto, T. &amp; Yoshida, M. Growth and reproduction of the benthic arrowworm Paraspadella gotoi (Chaetognatha) in laboratory culture. Invertebr. Reprod. Dev. <b>32<\/b>, 201\u2013207 (1997).<\/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 64\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Growth%20and%20reproduction%20of%20the%20benthic%20arrowworm%20Paraspadella%20gotoi%20%28Chaetognatha%29%20in%20laboratory%20culture&amp;journal=Invertebr.%20Reprod.%20Dev.&amp;volume=32&amp;pages=201-207&amp;publication_year=1997&amp;author=Goto%2CT&amp;author=Yoshida%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\">Green, M. R. &amp; Sambrook, J. Molecular Cloning. A Laboratory Manual 4th edn (2012).<\/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\">Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell <b>159<\/b>, 1665\u20131680 (2014).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXitFCrtrrK\" 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=25497547\" 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\/PMC5635824\" 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=A%203D%20map%20of%20the%20human%20genome%20at%20kilobase%20resolution%20reveals%20principles%20of%20chromatin%20looping&amp;journal=Cell&amp;volume=159&amp;pages=1665-1680&amp;publication_year=2014&amp;author=Rao%2CSSP\" 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\">Chapman, J. A. et al. Meraculous: de novo genome assembly with short paired-end reads. PLoS ONE <b>6<\/b>, e23501 (2011).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2011PLoSO...623501C\" aria-label=\"ADS reference 67\" target=\"_blank\">ADS<\/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%2BC3MXhtFOitrzO\" 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=21876754\" aria-label=\"PubMed reference 67\" 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\/PMC3158087\" aria-label=\"PubMed Central reference 67\" 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 67\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Meraculous%3A%20de%20novo%20genome%20assembly%20with%20short%20paired-end%20reads&amp;journal=PLoS%20ONE&amp;volume=6&amp;publication_year=2011&amp;author=Chapman%2CJA\" 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\">Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. <b>26<\/b>, 342\u2013350 (2016).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28XpvVClt78%3D\" 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=26848124\" 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\/PMC4772016\" 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=Chromosome-scale%20shotgun%20assembly%20using%20an%20in%20vitro%20method%20for%20long-range%20linkage&amp;journal=Genome%20Res.&amp;volume=26&amp;pages=342-350&amp;publication_year=2016&amp;author=Putnam%2CNH\" 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\">Simakov, O. et al. Deeply conserved synteny resolves early events in vertebrate evolution. Nat. Ecol. Evol. <b>4<\/b>, 820\u2013830 (2020).<\/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=32313176\" 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\/PMC7269912\" 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=Deeply%20conserved%20synteny%20resolves%20early%20events%20in%20vertebrate%20evolution&amp;journal=Nat.%20Ecol.%20Evol.&amp;volume=4&amp;pages=820-830&amp;publication_year=2020&amp;author=Simakov%2CO\" 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\">Rhie, A., Walenz, B. P., Koren, S. &amp; Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. <b>21<\/b>, 245 (2020).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhvVKmu7rF\" 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=32928274\" aria-label=\"PubMed reference 70\" 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\/PMC7488777\" aria-label=\"PubMed Central reference 70\" 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 70\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Merqury%3A%20reference-free%20quality%2C%20completeness%2C%20and%20phasing%20assessment%20for%20genome%20assemblies&amp;journal=Genome%20Biol.&amp;volume=21&amp;publication_year=2020&amp;author=Rhie%2CA&amp;author=Walenz%2CBP&amp;author=Koren%2CS&amp;author=Phillippy%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\">Sim\u00e3o, F. A., Waterhouse, R. M., Ioannidis, P., 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=\"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 71\" 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 71\" 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;volume=31&amp;pages=3210-3212&amp;publication_year=2015&amp;author=Sim%C3%A3o%2CFA&amp;author=Waterhouse%2CRM&amp;author=Ioannidis%2CP&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=\"72.\">\n<p class=\"c-article-references__text\" id=\"ref-CR72\">Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. <b>29<\/b>, 644\u2013652 (2011).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3MXmtV2hsbc%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=21572440\" 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\/PMC3571712\" 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=Full-length%20transcriptome%20assembly%20from%20RNA-Seq%20data%20without%20a%20reference%20genome&amp;journal=Nat.%20Biotechnol.&amp;volume=29&amp;pages=644-652&amp;publication_year=2011&amp;author=Grabherr%2CMG\" 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\">Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. <b>9<\/b>, R7 (2008).<\/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=18190707\" 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\/PMC2395244\" 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=Automated%20eukaryotic%20gene%20structure%20annotation%20using%20EVidenceModeler%20and%20the%20program%20to%20assemble%20spliced%20alignments&amp;journal=Genome%20Biol.&amp;volume=9&amp;publication_year=2008&amp;author=Haas%2CBJ\" 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\">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=\"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 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=16845043\" 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\/PMC1538822\" 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=AUGUSTUS%3A%20ab%20initio%20prediction%20of%20alternative%20transcripts&amp;journal=Nucleic%20Acids%20Res.&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=\"75.\">\n<p class=\"c-article-references__text\" id=\"ref-CR75\">Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. <b>47<\/b>, D309\u2013D314 (2019).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhs1Gqtr%2FL\" 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=30418610\" aria-label=\"PubMed reference 75\" 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 75\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=eggNOG%205.0%3A%20a%20hierarchical%2C%20functionally%20and%20phylogenetically%20annotated%20orthology%20resource%20based%20on%205090%20organisms%20and%202502%20viruses&amp;journal=Nucleic%20Acids%20Res.&amp;volume=47&amp;pages=D309-D314&amp;publication_year=2019&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=\"76.\">\n<p class=\"c-article-references__text\" id=\"ref-CR76\">Klopfenstein, D. V. et al. GOATOOLS: a Python library for Gene Ontology analyses. Sci Rep. <b>8<\/b>, 10872 (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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2018NatSR...810872K\" aria-label=\"ADS reference 76\" target=\"_blank\">ADS<\/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:STN:280:DC%2BB3c%2FpsFOmuw%3D%3D\" 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=30022098\" 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\/PMC6052049\" 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=GOATOOLS%3A%20a%20Python%20library%20for%20Gene%20Ontology%20analyses&amp;journal=Sci%20Rep.&amp;volume=8&amp;publication_year=2018&amp;author=Klopfenstein%2CDV\" 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\">Derelle, R., Philippe, H. &amp; Colbourne, J. K. Broccoli: combining phylogenetic and network analyses for orthology assignment. Mol. Biol. Evol. <b>37<\/b>, 3389\u20133396 (2020).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXht1amtLnF\" 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=32602888\" aria-label=\"PubMed reference 77\" 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 77\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Broccoli%3A%20combining%20phylogenetic%20and%20network%20analyses%20for%20orthology%20assignment&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=37&amp;pages=3389-3396&amp;publication_year=2020&amp;author=Derelle%2CR&amp;author=Philippe%2CH&amp;author=Colbourne%2CJK\" 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\">Katoh, K., Misawa, K., Kuma, K.-I. &amp; Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. <b>30<\/b>, 3059\u20133066 (2002).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD38XlslOqu7s%3D\" aria-label=\"CAS reference 78\" 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=12136088\" 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\/PMC135756\" 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=MAFFT%3A%20a%20novel%20method%20for%20rapid%20multiple%20sequence%20alignment%20based%20on%20fast%20Fourier%20transform&amp;journal=Nucleic%20Acids%20Res.&amp;volume=30&amp;pages=3059-3066&amp;publication_year=2002&amp;author=Katoh%2CK&amp;author=Misawa%2CK&amp;author=Kuma%2CK-I&amp;author=Miyata%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=\"79.\">\n<p class=\"c-article-references__text\" id=\"ref-CR79\">Steenwyk, J. L., Buida, T. J. 3rd, Li, Y., Shen, X.-X. &amp; Rokas, A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS Biol. <b>18<\/b>, e3001007 (2020).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXis1yku7rL\" 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=33264284\" 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\/PMC7735675\" 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=ClipKIT%3A%20a%20multiple%20sequence%20alignment%20trimming%20software%20for%20accurate%20phylogenomic%20inference&amp;journal=PLoS%20Biol.&amp;volume=18&amp;publication_year=2020&amp;author=Steenwyk%2CJL&amp;author=Buida%2CTJ&amp;author=Li%2CY&amp;author=Shen%2CX-X&amp;author=Rokas%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=\"80.\">\n<p class=\"c-article-references__text\" id=\"ref-CR80\">Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. &amp; Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. <b>32<\/b>, 268\u2013274 (2015).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2MXivFGltrs%3D\" aria-label=\"CAS reference 80\" 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=25371430\" aria-label=\"PubMed reference 80\" 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 80\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=IQ-TREE%3A%20a%20fast%20and%20effective%20stochastic%20algorithm%20for%20estimating%20maximum-likelihood%20phylogenies&amp;journal=Mol.%20Biol.%20Evol.&amp;volume=32&amp;pages=268-274&amp;publication_year=2015&amp;author=Nguyen%2CL-T&amp;author=Schmidt%2CHA&amp;author=Haeseler%2CA&amp;author=Minh%2CBQ\" 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\">Barrera-Redondo, J., Lotharukpong, J. S., Drost, H.-G. &amp; Coelho, S. M. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol. <b>24<\/b>, 54 (2023).<\/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=36964572\" aria-label=\"PubMed reference 81\" 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\/PMC10037820\" aria-label=\"PubMed Central reference 81\" 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 81\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Uncovering%20gene-family%20founder%20events%20during%20major%20evolutionary%20transitions%20in%20animals%2C%20plants%20and%20fungi%20using%20GenEra&amp;journal=Genome%20Biol.&amp;volume=24&amp;publication_year=2023&amp;author=Barrera-Redondo%2CJ&amp;author=Lotharukpong%2CJS&amp;author=Drost%2CH-G&amp;author=Coelho%2CSM\" 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\">Steinegger, M. &amp; S\u00f6ding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. <b>35<\/b>, 1026\u20131028 (2017).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhs1GqsLzE\" aria-label=\"CAS reference 82\" 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=29035372\" aria-label=\"PubMed reference 82\" 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 82\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=MMseqs2%20enables%20sensitive%20protein%20sequence%20searching%20for%20the%20analysis%20of%20massive%20data%20sets&amp;journal=Nat.%20Biotechnol.&amp;volume=35&amp;pages=1026-1028&amp;publication_year=2017&amp;author=Steinegger%2CM&amp;author=S%C3%B6ding%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=\"83.\">\n<p class=\"c-article-references__text\" id=\"ref-CR83\">Benton M. J., Donoghue P. C. J. &amp; Asher R. J. in The Timetree Of Life (ed. Kumar, S. B. H.) 35\u201386 (Oxford Univ. Press, 2009).<\/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\">Rota-Stabelli, O., Daley, A. C. &amp; Pisani, D. Molecular timetrees reveal a Cambrian colonization of land and a new scenario for ecdysozoan evolution. Curr. Biol. <b>23<\/b>, 392\u2013398 (2013).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3sXhvFWjuro%3D\" aria-label=\"CAS reference 84\" 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=23375891\" aria-label=\"PubMed reference 84\" 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 84\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Molecular%20timetrees%20reveal%20a%20Cambrian%20colonization%20of%20land%20and%20a%20new%20scenario%20for%20ecdysozoan%20evolution&amp;journal=Curr.%20Biol.&amp;volume=23&amp;pages=392-398&amp;publication_year=2013&amp;author=Rota-Stabelli%2CO&amp;author=Daley%2CAC&amp;author=Pisani%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=\"85.\">\n<p class=\"c-article-references__text\" id=\"ref-CR85\">Vannier, J., Steiner, M., Renvois\u00e9, E., Hu, S.-X. &amp; Casanova, J.-P. Early Cambrian origin of modern food webs: evidence from predator arrow worms. Proc. Biol. Sci. <b>274<\/b>, 627\u2013633 (2007).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:STN:280:DC%2BD2s7is1Ggtw%3D%3D\" aria-label=\"CAS reference 85\" 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=17254986\" aria-label=\"PubMed reference 85\" 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 85\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Early%20Cambrian%20origin%20of%20modern%20food%20webs%3A%20evidence%20from%20predator%20arrow%20worms&amp;journal=Proc.%20Biol.%20Sci.&amp;volume=274&amp;pages=627-633&amp;publication_year=2007&amp;author=Vannier%2CJ&amp;author=Steiner%2CM&amp;author=Renvois%C3%A9%2CE&amp;author=Hu%2CS-X&amp;author=Casanova%2CJ-P\" 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=\"86.\">\n<p class=\"c-article-references__text\" id=\"ref-CR86\">Mendes, F. K., Vanderpool, D., Fulton, B. &amp; Hahn, M. W. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics <b>36<\/b>, 5516\u20135518 (2021).<\/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=33325502\" aria-label=\"PubMed reference 86\" 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 86\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=CAFE%205%20models%20variation%20in%20evolutionary%20rates%20among%20gene%20families&amp;journal=Bioinformatics&amp;volume=36&amp;pages=5516-5518&amp;publication_year=2021&amp;author=Mendes%2CFK&amp;author=Vanderpool%2CD&amp;author=Fulton%2CB&amp;author=Hahn%2CMW\" 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=\"87.\">\n<p class=\"c-article-references__text\" id=\"ref-CR87\">Matus, D. Q., Halanych, K. M. &amp; Martindale, M. Q. The Hox gene complement of a pelagic chaetognath, Flaccisagitta enflata. Integr. Comp. Biol. <b>47<\/b>, 854 (2007).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1cXisl2jtA%3D%3D\" aria-label=\"CAS reference 87\" 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=21669764\" aria-label=\"PubMed reference 87\" 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 87\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20Hox%20gene%20complement%20of%20a%20pelagic%20chaetognath%2C%20Flaccisagitta%20enflata&amp;journal=Integr.%20Comp.%20Biol.&amp;volume=47&amp;publication_year=2007&amp;author=Matus%2CDQ&amp;author=Halanych%2CKM&amp;author=Martindale%2CMQ\" 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=\"88.\">\n<p class=\"c-article-references__text\" id=\"ref-CR88\">Open2C, et al. Pairtools: from sequencing data to chromosome contacts. PLoS Comput. Biol. <b>20<\/b>, e1012164 (2024).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"89.\">\n<p class=\"c-article-references__text\" id=\"ref-CR89\">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=\"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 89\" 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 89\" 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 89\" 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 89\" 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;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=\"90.\">\n<p class=\"c-article-references__text\" id=\"ref-CR90\">Knight, P. A. &amp; Ruiz, D. A fast algorithm for matrix balancing. IMA J. Numer. Anal. <b>33<\/b>, 1029\u20131047 (2013).<\/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=\"mathscinet reference\" data-track-action=\"mathscinet reference\" href=\"http:\/\/www.ams.org\/mathscinet-getitem?mr=3081493\" aria-label=\"MathSciNet reference 90\" target=\"_blank\">MathSciNet<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"math reference\" data-track-action=\"math reference\" href=\"http:\/\/www.emis.de\/MATH-item?1276.65025\" aria-label=\"MATH reference 90\" target=\"_blank\">MATH<\/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 90\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20fast%20algorithm%20for%20matrix%20balancing&amp;journal=IMA%20J.%20Numer.%20Anal.&amp;volume=33&amp;pages=1029-1047&amp;publication_year=2013&amp;author=Knight%2CPA&amp;author=Ruiz%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=\"91.\">\n<p class=\"c-article-references__text\" id=\"ref-CR91\">Kruse, K., Hug, C. B. &amp; Vaquerizas, J. M. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol. <b>21<\/b>, 303 (2020).<\/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=33334380\" aria-label=\"PubMed reference 91\" 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\/PMC7745377\" aria-label=\"PubMed Central reference 91\" 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 91\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=FAN-C%3A%20a%20feature-rich%20framework%20for%20the%20analysis%20and%20visualisation%20of%20chromosome%20conformation%20capture%20data&amp;journal=Genome%20Biol.&amp;volume=21&amp;publication_year=2020&amp;author=Kruse%2CK&amp;author=Hug%2CCB&amp;author=Vaquerizas%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=\"92.\">\n<p class=\"c-article-references__text\" id=\"ref-CR92\">Marl\u00e9taz, F. et al. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. Cell Genomics <b>3<\/b>, 100295 (2023).<\/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=37082140\" aria-label=\"PubMed reference 92\" 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\/PMC10112332\" aria-label=\"PubMed Central reference 92\" 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 92\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Analysis%20of%20the%20P.%20lividus%20sea%20urchin%20genome%20highlights%20contrasting%20trends%20of%20genomic%20and%20regulatory%20evolution%20in%20deuterostomes&amp;journal=Cell%20Genomics&amp;volume=3&amp;publication_year=2023&amp;author=Marl%C3%A9taz%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=\"93.\">\n<p class=\"c-article-references__text\" id=\"ref-CR93\">Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods <b>14<\/b>, 959\u2013962 (2017).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhtl2gtL7F\" aria-label=\"CAS reference 93\" 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=28846090\" aria-label=\"PubMed reference 93\" 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\/PMC5623106\" aria-label=\"PubMed Central reference 93\" 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 93\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=An%20improved%20ATAC-seq%20protocol%20reduces%20background%20and%20enables%20interrogation%20of%20frozen%20tissues&amp;journal=Nat.%20Methods&amp;volume=14&amp;pages=959-962&amp;publication_year=2017&amp;author=Corces%2CMR\" 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=\"94.\">\n<p class=\"c-article-references__text\" id=\"ref-CR94\">Langmead, B. &amp; Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods <b>9<\/b>, 357\u2013359 (2012).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38Xjt1Oqt7c%3D\" aria-label=\"CAS reference 94\" 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=22388286\" aria-label=\"PubMed reference 94\" 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\/PMC3322381\" aria-label=\"PubMed Central reference 94\" 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 94\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Fast%20gapped-read%20alignment%20with%20Bowtie%202&amp;journal=Nat.%20Methods&amp;volume=9&amp;pages=357-359&amp;publication_year=2012&amp;author=Langmead%2CB&amp;author=Salzberg%2CSL\" 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=\"95.\">\n<p class=\"c-article-references__text\" id=\"ref-CR95\">Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell <b>38<\/b>, 576\u2013589 (2010).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3cXns1SlsLc%3D\" aria-label=\"CAS reference 95\" 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=20513432\" aria-label=\"PubMed reference 95\" 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\/PMC2898526\" aria-label=\"PubMed Central reference 95\" 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 95\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Simple%20combinations%20of%20lineage-determining%20transcription%20factors%20prime%20cis-regulatory%20elements%20required%20for%20macrophage%20and%20B%20cell%20identities&amp;journal=Mol.%20Cell&amp;volume=38&amp;pages=576-589&amp;publication_year=2010&amp;author=Heinz%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=\"96.\">\n<p class=\"c-article-references__text\" id=\"ref-CR96\">Wenzel, M. A., M\u00fcller, B. &amp; Pettitt, J. SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-seq data. BMC Bioinformatics <b>22<\/b>, 140 (2021).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXht1WrtbbP\" aria-label=\"CAS reference 96\" 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=33752599\" aria-label=\"PubMed reference 96\" 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\/PMC7986045\" aria-label=\"PubMed Central reference 96\" 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 96\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=SLIDR%20and%20SLOPPR%3A%20flexible%20identification%20of%20spliced%20leader%20trans-splicing%20and%20prediction%20of%20eukaryotic%20operons%20from%20RNA-seq%20data&amp;journal=BMC%20Bioinformatics&amp;volume=22&amp;publication_year=2021&amp;author=Wenzel%2CMA&amp;author=M%C3%BCller%2CB&amp;author=Pettitt%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=\"97.\">\n<p class=\"c-article-references__text\" id=\"ref-CR97\">Liao, Y., Smyth, G. K. &amp; Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics <b>30<\/b>, 923\u2013930 (2014).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXltFGqu7c%3D\" aria-label=\"CAS reference 97\" 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=24227677\" aria-label=\"PubMed reference 97\" 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 97\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=featureCounts%3A%20an%20efficient%20general%20purpose%20program%20for%20assigning%20sequence%20reads%20to%20genomic%20features&amp;journal=Bioinformatics&amp;volume=30&amp;pages=923-930&amp;publication_year=2014&amp;author=Liao%2CY&amp;author=Smyth%2CGK&amp;author=Shi%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=\"98.\">\n<p class=\"c-article-references__text\" id=\"ref-CR98\">Hao, Y. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Biotechnol. <b>42<\/b>, 293\u2013304 (2024).<\/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=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXhtFSisbvO\" aria-label=\"CAS reference 98\" 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=37231261\" aria-label=\"PubMed reference 98\" 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 98\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Dictionary%20learning%20for%20integrative%2C%20multimodal%20and%20scalable%20single-cell%20analysis&amp;journal=Nat.%20Biotechnol.&amp;volume=42&amp;pages=293-304&amp;publication_year=2024&amp;author=Hao%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=\"99.\">\n<p class=\"c-article-references__text\" id=\"ref-CR99\">Kryuchkova-Mostacci, N. &amp; Robinson-Rechavi, M. A benchmark of gene expression tissue-specificity metrics. Brief. Bioinformatics <b>18<\/b>, 205\u2013214 (2016).<\/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 99\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20benchmark%20of%20gene%20expression%20tissue-specificity%20metrics&amp;journal=Brief.%20Bioinformatics&amp;volume=18&amp;pages=205-214&amp;publication_year=2016&amp;author=Kryuchkova-Mostacci%2CN&amp;author=Robinson-Rechavi%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=\"100.\">\n<p class=\"c-article-references__text\" id=\"ref-CR100\">Garc\u00eda-Castro, H. et al. ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biol. <b>22<\/b>, 89 (2021).<\/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=33827654\" aria-label=\"PubMed reference 100\" 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\/PMC8028764\" aria-label=\"PubMed Central reference 100\" 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 100\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=ACME%20dissociation%3A%20a%20versatile%20cell%20fixation-dissociation%20method%20for%20single-cell%20transcriptomics&amp;journal=Genome%20Biol.&amp;volume=22&amp;publication_year=2021&amp;author=Garc%C3%ADa-Castro%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=\"101.\">\n<p class=\"c-article-references__text\" id=\"ref-CR101\">Hejnol, A. &amp; Martindale, M. Q. Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature <b>456<\/b>, 382\u2013386 (2008).<\/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=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2008Natur.456..382H\" aria-label=\"ADS reference 101\" target=\"_blank\">ADS<\/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%2BD1cXhsVSjsLnM\" aria-label=\"CAS reference 101\" 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=18806777\" aria-label=\"PubMed reference 101\" 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 101\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Acoel%20development%20indicates%20the%20independent%20evolution%20of%20the%20bilaterian%20mouth%20and%20anus&amp;journal=Nature&amp;volume=456&amp;pages=382-386&amp;publication_year=2008&amp;author=Hejnol%2CA&amp;author=Martindale%2CMQ\" 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=\"102.\">\n<p class=\"c-article-references__text\" id=\"ref-CR102\">Hejnol, A. In situ protocol for embryos and juveniles of Convolutriloba longifissura. Protoc. Exch. <a href=\"https:\/\/doi.org\/10.1038\/nprot.2008.201\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1038\/nprot.2008.201\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.1038\/nprot.2008.201<\/a> (2008).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"103.\">\n<p class=\"c-article-references__text\" id=\"ref-CR103\">Marl\u00e9taz, F. et al. The genomic origin of the unique chaetognath body plan [Data set]. Zenodo <a href=\"https:\/\/doi.org\/10.5281\/zenodo.13936459\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.5281\/zenodo.13936459\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.5281\/zenodo.13936459<\/a> (2024).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\" data-counter=\"104.\">\n<p class=\"c-article-references__text\" id=\"ref-CR104\">G\u0105siorowski, L., Mart\u00edn-Dur\u00e1n, J. M. &amp; Hejnolin, A. in Hox Modules in Evolution and Development (ed. Ferrier, D. E. K.) 177\u2013194 (CRC, 2023).<\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Erwin, D. H. The origin of animal body plans: a view from fossil evidence and the regulatory genome.&hellip;\n","protected":false},"author":2,"featured_media":342975,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[104506,88933,3965,3966,37581,70,16,15],"class_list":{"0":"post-342974","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-evolutionary-developmental-biology","9":"tag-genome-evolution","10":"tag-humanities-and-social-sciences","11":"tag-multidisciplinary","12":"tag-phylogenetics","13":"tag-science","14":"tag-uk","15":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/115025298509018164","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/342974","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=342974"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/342974\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/342975"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=342974"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=342974"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=342974"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}