{"id":38517,"date":"2025-09-02T11:48:17","date_gmt":"2025-09-02T11:48:17","guid":{"rendered":"https:\/\/www.europesays.com\/ie\/38517\/"},"modified":"2025-09-02T11:48:17","modified_gmt":"2025-09-02T11:48:17","slug":"chromosome-level-genome-assembly-of-the-tyrrhenian-tree-frog-hyla-sarda","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/ie\/38517\/","title":{"rendered":"Chromosome-level genome assembly of the Tyrrhenian tree frog (Hyla sarda)"},"content":{"rendered":"
  • \n

    Bernini, F., Doria, G., Razzetti, E. & Sindaco, R. Atlas of Italian Amphibians and Reptiles. (Societas Herpetologica Italica, Polistampa, 2006).<\/p>\n<\/li>\n

  • \n

    Lanza, B., Andreone, F., Bologna, M. A., Corti, C. & Razzetti, E. Amphibia. Fauna d\u2019Italia (Calderini, 2007).<\/p>\n<\/li>\n

  • \n

    Romano, A. et al. Hyla sarda. The IUCN Red List of Threatened Species 2024, e.T55645A223764163 https:\/\/doi.org\/10.2305\/IUCN.UK.2024-2.RLTS.T55645A223764163.en<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Bisconti, R., Canestrelli, D. & Nascetti, G. Genetic diversity and evolutionary history of the Tyrrhenian treefrog Hyla sarda (Anura: Hylidae): adding pieces to the puzzle of Corsica-Sardinia biota. Biological Journal of The Linnean Society 103<\/b>, 159\u2013167, https:\/\/doi.org\/10.1111\/j.1095-8312.2011.01643.x<\/a> (2011).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bisconti, R., Canestrelli, D., Colangelo, P. & Nascetti, G. Multiple lines of evidence for demographic and range expansion of a temperate species (Hyla sarda) during the last glaciation. Mol. Ecol. 20<\/b>, 5313\u20135327, https:\/\/doi.org\/10.1111\/j.1365-294X.2011.05363.x<\/a> (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Spadavecchia, G., Chiocchio, A., Bisconti, R. & Canestrelli, D. Paso doble: A two-step Late Pleistocene range expansion in the Tyrrhenian tree frog Hyla sarda. Gene 780<\/b>, 145489, https:\/\/doi.org\/10.1016\/j.gene.2021.145489<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bisconti, R., Chiocchio, A., Costantini, D., Carere, C. & Canestrelli, D. Drivers of phenotypic variation along a Late Pleistocene range expansion route. J. Biogeogr.e70044, https:\/\/doi.org\/10.1111\/jbi.70044<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Spadavecchia, G. et al. Spatial differentiation of background matching strategies along a Late Pleistocene range expansion route. Evol. Ecol. 37<\/b>, 291\u2013303, https:\/\/doi.org\/10.1007\/s10682-022-10216-2<\/a> (2023).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liparoto, A., Canestrelli, D., Bisconti, R., Carere, C. & Costantini, D. Biogeographic history moulds population differentiation in ageing of oxidative status in an amphibian. J. Exp. Biol. 223<\/b>, jeb235002, https:\/\/doi.org\/10.1242\/jeb.235002<\/a> (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Canestrelli, D. et al. Biogeography of telomere dynamics in a vertebrate. Ecography (Cop.) 44<\/b>, 453\u2013455, https:\/\/doi.org\/10.1111\/ecog.05286<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bisconti, R. et al. Evolution of personality and locomotory performance traits during a Late Pleistocene island colonization in a tree frog. Curr. Zool. 69<\/b>, 631\u2013641, https:\/\/doi.org\/10.1093\/cz\/zoac062<\/a> (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kosch, T. A. et al. Comparative analysis of amphibian genomes: An emerging resource for basic and applied research. Mol. Ecol. Resour. 25<\/b>, e14025, https:\/\/doi.org\/10.1111\/1755-0998.14025<\/a> (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Challis, R., Kumar, S., Sotero-Caio, C., Brown, M. & Blaxter, M. Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Wellcome Open Res 8<\/b>, 24, https:\/\/doi.org\/10.12688\/wellcomeopenres.18658.1<\/a> (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Morescalchi, A. Evolution and karyology of the amphibians. Boll. Zool. 47<\/b>, 113\u2013126, https:\/\/doi.org\/10.1080\/11250008009438709<\/a> (1980).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bredeson, J. V. et al. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat. Commun. 15<\/b>, 579, https:\/\/doi.org\/10.1038\/s41467-023-43012-9<\/a> (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jeffries, D. L. et al. A rapid rate of sex-chromosome turnover and non-random transitions in true frogs. Nat. Commun. 9<\/b>, 4088, https:\/\/doi.org\/10.1038\/s41467-018-06517-2<\/a> (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dufresnes, C., Brelsford, A., Baier, F. & Perrin, N. When sex chromosomes recombine only in the heterogametic sex: Heterochiasmy and heterogamety in Hyla tree frogs. Mol. Biol. Evol. 38<\/b>, 192\u2013200, https:\/\/doi.org\/10.1093\/molbev\/msaa201<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rhie, A. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592<\/b>, 737\u2013746, https:\/\/doi.org\/10.1038\/s41586-021-03451-0<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Libro, P. et al. First brain de novo transcriptome of the Tyrrhenian tree frog, Hyla sarda, for the study of dispersal behavior. Front. Ecol. Evol. 10<\/b>, 947186, https:\/\/doi.org\/10.3389\/fevo.2022.947186<\/a> (2022).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Larivi\u00e8re, D. et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat. Biotechnol. 42<\/b>, 367\u2013370, https:\/\/doi.org\/10.1038\/s41587-023-02100-3<\/a> (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21<\/b>, 245, https:\/\/doi.org\/10.1186\/s13059-020-02134-9<\/a> (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11<\/b>, 1432, https:\/\/doi.org\/10.1038\/s41467-020-14998-3<\/a> (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18<\/b>, 170\u2013175, https:\/\/doi.org\/10.1038\/s41592-020-01056-5<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bocklandt, S., Hastie, A. & Cao, H. Bionano genome mapping: High-throughput, ultra-long molecule genome analysis system for precision genome assembly and haploid-resolved structural variation discovery. in Single molecule and single cell sequencing. Advances in Experimental Medicine and Biology, vol 1129 (ed. Suzuki, Y.) 97-118 https:\/\/doi.org\/10.1007\/978-981-13-6037-4_7<\/a> (Springer, Singapore, 2019).<\/p>\n<\/li>\n

  • \n

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 https:\/\/doi.org\/10.48550\/arXiv.1303.3997<\/a> (2013).<\/p>\n<\/li>\n

  • \n

    Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25<\/b>, 2078\u20132079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352<\/a> (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39<\/b>, btac808, https:\/\/doi.org\/10.1093\/bioinformatics\/btac808<\/a> (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Howe, K. et al. Significantly improving the quality of genome assemblies through curation. Gigascience 10<\/b>, giaa153, https:\/\/doi.org\/10.1093\/gigascience\/giaa153<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vertebrate Genomes Project & NCBI RefSeq Hyla sarda genome assembly aHylSar1.hap1. NCBI GenBank http:\/\/identifiers.org\/assembly:GCF_029499605.1<\/a> (2023)<\/p>\n<\/li>\n

  • \n

    Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome research 19<\/b>, 1639\u20131645, http:\/\/www.genome.org\/cgi\/doi\/10.1101\/gr.092759.109<\/a> (2009).<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Baril, T., Galbraith, J. & Hayward, A. Earl Grey: A fully automated user-friendly transposable element annotation and analysis pipeline. Mol. Biol. Evol. 41<\/b>, msae068, https:\/\/doi.org\/10.1093\/molbev\/msae068<\/a> (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. USA. 117<\/b>, 9451\u20139457, https:\/\/doi.org\/10.1073\/pnas.1921046117<\/a> (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0. 2013-2015. (2015).<\/p>\n<\/li>\n

  • \n

    Storer, J., Hubley, R., Rosen, J., Wheeler, T. J. & Smit, A. F. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob. DNA 12<\/b>, 1\u201314, https:\/\/doi.org\/10.1186\/s13100-020-00230-y<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6<\/b>, 1\u20136, https:\/\/doi.org\/10.1186\/s13100-015-0041-9<\/a> (2015).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Thibaud-Nissen, F., Souvorov, A., Murphy, T. D., DiCuccio, M. & Kitts, P. P8008 the NCBI eukaryotic genome annotation pipeline. Journal of Animal Science 94<\/b>, 184\u2013184, https:\/\/doi.org\/10.2527\/jas2016.94supplement4184x<\/a> (2016).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sim\u00e3o, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31<\/b>, 3210\u20133212, https:\/\/doi.org\/10.1093\/bioinformatics\/btv351<\/a> (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Manni, M., Berkeley, M. R., Seppey, M., Sim\u00e3o, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38<\/b>, 4647\u20134654, https:\/\/doi.org\/10.1093\/molbev\/msab199<\/a> (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kriventseva, E. V. et al. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res. 47<\/b>, D807\u2013D811, https:\/\/doi.org\/10.1093\/nar\/gky1053<\/a> (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nevers, Y. et al. Quality assessment of gene repertoire annotations with OMArk. Nat. Biotechnol. 43<\/b>, 124\u2013133, https:\/\/doi.org\/10.1038\/s41587-024-02147-w<\/a> (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Uliano-Silva, M. et al. MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics 24<\/b>, 288, https:\/\/doi.org\/10.1186\/s12859-023-05385-y<\/a> (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Allio, R. et al. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol. Ecol. Resour. 20<\/b>, 892\u2013905, https:\/\/doi.org\/10.1111\/1755-0998.13160<\/a> (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hyla annectans mitochondrion, complete genome. NCBI GenBank http:\/\/identifiers.org\/insdc:KM271781.1<\/a> (2019)<\/p>\n<\/li>\n

  • \n

    Vertebrate Genomes Project. Hyla sarda genome assembly aHylSar1.hap2. NCBI GenBank http:\/\/identifiers.org\/assembly:GCA_029493135.1<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Hyla sarda isolate aHylSar1 mitochondrion, complete sequence, whole genome shotgun sequence. NCBI GenBank http:\/\/identifiers.org\/insdc:CM056048.1<\/a> (2023)<\/p>\n<\/li>\n

  • \n

    Formenti, G. et al. Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics 38<\/b>, 4214\u20134216, https:\/\/doi.org\/10.1093\/bioinformatics\/btac460<\/a> (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Brown, M. R., Gonzalez de La Rosa, P. & Blaxter, M. tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. Bioinformatics 41<\/b>, btaf049, https:\/\/doi.org\/10.1093\/bioinformatics\/btaf049<\/a> (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Bernini, F., Doria, G., Razzetti, E. & Sindaco, R. Atlas of Italian Amphibians and Reptiles. (Societas Herpetologica Italica,…\n","protected":false},"author":2,"featured_media":38518,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[77],"tags":[6130,18,8101,1099,19,17,1100,133],"class_list":{"0":"post-38517","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-ecology","9":"tag-eire","10":"tag-evolution","11":"tag-humanities-and-social-sciences","12":"tag-ie","13":"tag-ireland","14":"tag-multidisciplinary","15":"tag-science"},"share_on_mastodon":{"url":"","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/38517","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=38517"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/38517\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/38518"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=38517"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=38517"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=38517"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}