{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T18:44:58Z","timestamp":1792089898698,"version":"4.4.0"},"reference-count":133,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["R35 GM144336"],"award-info":[{"award-number":["R35 GM144336"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"name":"LOEWE\u2013Landes-Offensive zur Entwicklung Wissenschaftlich-\u00f6konomischer Exzellenz","award":["LOEWE\/1\/10\/519\/03\/03.001(0014)\/52"],"award-info":[{"award-number":["LOEWE\/1\/10\/519\/03\/03.001(0014)\/52"]}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["R35 GM144336"],"award-info":[{"award-number":["R35 GM144336"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"name":"LOEWE\u2013Landes-Offensive zur Entwicklung Wissenschaftlich-\u00f6konomischer Exzellenz","award":["LOEWE\/1\/10\/519\/03\/03.001(0014)\/52"],"award-info":[{"award-number":["LOEWE\/1\/10\/519\/03\/03.001(0014)\/52"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Notothenioids are a well characterised species flock endemic to the Antarctic and an important model group for studying genome adaptation to extreme cold. A new reference assembly and clade-wide comparative genomic analysis allow for investigation of cryonotothenioid evolution and the appearance of novel functionalities linked to cold adaptation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A new phased assembly of a model notothenioid,\n                      <jats:italic>Harpagifer antarcticus<\/jats:italic>\n                      , demonstrated low levels of haplotypic variability across the genome. Nevertheless, numerous insertions from multiple LINE-L2 clades were found, suggesting ongoing transposition with potential contribution to speciation. Contrary to expectations the\n                      <jats:italic>afgp<\/jats:italic>\n                      locus was highly similar between haplotypes, except for large length allelic variants of afgp genes. Analysis suggests a model for the\n                      <jats:italic>afgp<\/jats:italic>\n                      locus expansion in\n                      <jats:italic>H. antarcticus<\/jats:italic>\n                      through segmental tandem duplications involving two pairs of\n                      <jats:italic>afgp<\/jats:italic>\n                      genes at time. Syntenic reconstruction of genomes from across the clade demonstrates conserved macrosyntenic relationships and group specific chromosomal fusions of notothenioids. Quantification of genome gain and transposition rates during cryonotothenioid diversification showed a first ancestral slow genome expansion concurrent with historic temperature drops. This was followed by lineage-specific massive peaks of genomic gain and transposition activity. Finally, we identified a set of genes that underwent ancestral diversifying selection and acquired novel conserved non-coding elements during the cryonotothenioid emergence. These were related to antioxidants and proteostasis, which may have facilitated the notothenioid Antarctic radiation.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Diversifying selection and genomic gain linked to transposon activity are primary contributors to lineage-specific evolutionary dynamics through the clade which facilitated adaptation to life in the cold.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13059-026-04293-7","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T14:30:37Z","timestamp":1792074637000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation"],"prefix":"10.1186","volume":"27","author":[{"given":"Jacopo","family":"Martelossi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ksenia","family":"Krasheninnikova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy","family":"Denton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan M. D.","family":"Wood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas C.","family":"Mathers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Durbin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nova","family":"Fong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Bentley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melody S.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iliana","family":"Bista","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"4293_CR1","doi-asserted-by":"publisher","unstructured":"Lecointre G, Am\u00e9ziane N, Boisselier M-C, Bonillo C, Busson F, Causse R, et al. Is the Species Flock Concept Operational? The Antarctic Shelf Case. PLOS ONE. 2013;8:e68787. https:\/\/doi.org\/10.1371\/journal.pone.0068787. Public Library of Science. Cited 2026 Jan 9.","DOI":"10.1371\/journal.pone.0068787"},{"key":"4293_CR2","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1017\/S0954102020000632","volume":"33","author":"JT Eastman","year":"2021","unstructured":"Eastman JT, Eakin RR. Checklist of the species of notothenioid fishes. Antarct Sci. 2021;33:273\u201380. https:\/\/doi.org\/10.1017\/S0954102020000632.","journal-title":"Antarct Sci"},{"key":"4293_CR3","doi-asserted-by":"publisher","unstructured":"Di Prisco G, Pisano E, Clarke A. Fishes of Antarctica: a biological overview Edited by G. di Prisco, E. Pisano & A. Clarke Springer-Verlag, Milano (1998). 363 pages. Price DM 198. ISBN 88 470 0028 9. Antarctic Sci. 1999;11:379\u201380. https:\/\/doi.org\/10.1017\/S0954102099210462. Cited 2026 Jan 15.","DOI":"10.1017\/S0954102099210462"},{"key":"4293_CR4","doi-asserted-by":"publisher","unstructured":"Chen L, DeVries AL, Cheng C-HC. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid\u2009fish. Proceedings of the National Academy of Sciences. Proc Natl Acad Sci. 1997;94:3811\u20136. https:\/\/doi.org\/10.1073\/pnas.94.8.3811. Cited 2026 Jan 14.","DOI":"10.1073\/pnas.94.8.3811"},{"key":"4293_CR5","doi-asserted-by":"publisher","unstructured":"Cao L, Huang Q, Wu Z, Cao D, Ma Z, Xu Q, et al. Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids. Nat Commun. 2016;7:12987. https:\/\/doi.org\/10.1038\/ncomms12987. Nature Publishing Group. Cited 2026 July 27.","DOI":"10.1038\/ncomms12987"},{"key":"4293_CR6","doi-asserted-by":"publisher","unstructured":"Berthelot C, Clarke J, Desvignes T, William Detrich H III, Flicek P, Peck LS, et al. Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? Genome Biol Evol. 2019;11:220\u201331. https:\/\/doi.org\/10.1093\/gbe\/evy262. Cited 2025 Nov 19.","DOI":"10.1093\/gbe\/evy262"},{"key":"4293_CR7","unstructured":"Bista I, Wood JM, Desvignes T, McCarthy SA, Matschiner M, Ning Z, et al. Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nature communications. 2023;14:3412. https:\/\/www.nature.com\/articles\/s41467-023-38567-6. Nature Publishing Group UK London. Cited 2025 Aug 25."},{"key":"4293_CR8","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/46721","volume":"401","author":"C-HC Cheng","year":"1999","unstructured":"Cheng C-HC, Chen L. Evolution of an antifreeze glycoprotein. Nature. 1999;401:443\u20134. https:\/\/doi.org\/10.1038\/46721.","journal-title":"Nature"},{"key":"4293_CR9","doi-asserted-by":"publisher","unstructured":"Nicodemus-Johnson J, Silic S, Ghigliotti L, Pisano E, Cheng C-HC. Assembly of the antifreeze glycoprotein\/trypsinogen-like protease genomic locus in the Antarctic toothfish Dissostichus mawsoni (Norman). Genomics. 2011;98:194\u2013201. https:\/\/doi.org\/10.1016\/j.ygeno.2011.06.002. Cited 2025 Nov 30.","DOI":"10.1016\/j.ygeno.2011.06.002"},{"key":"4293_CR10","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad029","volume":"40","author":"AG Rivera-Col\u00f3n","year":"2023","unstructured":"Rivera-Col\u00f3n AG, Rayamajhi N, Minhas BF, Madrigal G, Bilyk KT, Yoon V, et al. Genomics of secondarily temperate adaptation in the only non-Antarctic icefish. Mol Biol Evol. 2023;40:msad029. https:\/\/doi.org\/10.1093\/molbev\/msad029.","journal-title":"Mol Biol Evol"},{"key":"4293_CR11","doi-asserted-by":"publisher","unstructured":"Ryder D, Stone D, Minardi D, Riley A, Avant J, Cross L, et al. De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics. 2024;25:233. https:\/\/doi.org\/10.1186\/s12864-024-10141-4. Cited 2026 Jan 15.","DOI":"10.1186\/s12864-024-10141-4"},{"key":"4293_CR12","doi-asserted-by":"publisher","unstructured":"Fraser KPP, Peck LS, Clark MS, Clarke A, Hill SL. Life in the freezer: protein metabolism in Antarctic fish. R Soc Open Sci. 2022;9:211272. https:\/\/doi.org\/10.1098\/rsos.211272. Cited 2026 Jan 15.","DOI":"10.1098\/rsos.211272"},{"key":"4293_CR13","doi-asserted-by":"publisher","unstructured":"Fraser KPP, Peck LS, Clark MS, Clarke A. A comparative study of tissue protein synthesis rates in an Antarctic, Harpagifer antarcticus and a temperate, Lipophrys pholis teleost. Compar Biochem Physiol Part A Mol Integ Physiol. 2024;295:111650. https:\/\/doi.org\/10.1016\/j.cbpa.2024.111650. Cited 2026 Jan 9.","DOI":"10.1016\/j.cbpa.2024.111650"},{"key":"4293_CR14","doi-asserted-by":"publisher","unstructured":"Marty A-PM, Ward EN, Lamb JR, van Tartwijk FW, Peck LS, Clark MS, et al. A High-Resolution Microscopy System for Biological Studies of Cold-Adapted Species Under Physiological Conditions. Small Methods. 2025;9:2401682. https:\/\/doi.org\/10.1002\/smtd.202401682. Cited 2026 Mar 2","DOI":"10.1002\/smtd.202401682"},{"key":"4293_CR15","doi-asserted-by":"publisher","unstructured":"Detrich HW, Stuart A, Schoenborn M, Parker SK, Meth\u00e9 BA, Amemiya CT. Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa. J Exp Zoology Part B Mol Dev Evol. 2010;314B:369\u201381. https:\/\/doi.org\/10.1002\/jez.b.21341. Cited 2025 Nov 12.","DOI":"10.1002\/jez.b.21341"},{"key":"4293_CR16","doi-asserted-by":"publisher","unstructured":"Chen L, Lu Y, Li W, Ren Y, Yu M, Jiang S, et al. The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. Gigascience. 2019;8:giz016. https:\/\/doi.org\/10.1093\/gigascience\/giz016. Cited 2026 Jan 14.","DOI":"10.1093\/gigascience\/giz016"},{"key":"4293_CR17","doi-asserted-by":"publisher","unstructured":"Auvinet J, Gra\u00e7a P, Ghigliotti L, Pisano E, Detta\u00ef A, Ozouf-Costaz C, et al. Insertion Hot Spots of DIRS1 Retrotransposon and Chromosomal Diversifications among the Antarctic Teleosts Nototheniidae. Int J Mol Sci. 2019;20:701. https:\/\/doi.org\/10.3390\/ijms20030701. Multidisciplinary Digital Publishing Institute. Cited 2026 Jan 14.","DOI":"10.3390\/ijms20030701"},{"key":"4293_CR18","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1002\/9781394312467.ch5","volume-title":"Transposable elements and genome evolution","author":"M Coronado-Zamora","year":"2024","unstructured":"Coronado-Zamora M, Gonz\u00e1lez J. Transposable elements and adaptation. In: Transposable elements and genome evolution. John Wiley & Sons, Ltd; 2024. p. 115\u201333. https:\/\/doi.org\/10.1002\/9781394312467.ch5."},{"key":"4293_CR19","doi-asserted-by":"publisher","unstructured":"Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, et al. Ten things you should know about transposable elements. Genome Biol. 2018;19:199. https:\/\/doi.org\/10.1186\/s13059-018-1577-z. Cited 2026 Feb 5.","DOI":"10.1186\/s13059-018-1577-z"},{"key":"4293_CR20","doi-asserted-by":"publisher","unstructured":"Rey O, Danchin E, Mirouze M, Loot C, Blanchet S. Adaptation to Global Change: A Transposable Element\u2013Epigenetics Perspective. Trends Ecol Evol. 2016;31:514\u201326. https:\/\/doi.org\/10.1016\/j.tree.2016.03.013. Cited 2026 Jan 14.","DOI":"10.1016\/j.tree.2016.03.013"},{"key":"4293_CR21","doi-asserted-by":"publisher","unstructured":"Xu H, Fang C, Xu W, Wang C, Song Y, Zhu C, et al. Evolution and genetic adaptation of fishes to the deep sea. Cell. 2025;188:1393\u20131408.e13. https:\/\/doi.org\/10.1016\/j.cell.2025.01.002. Elsevier. Cited 2026 Jan 14.","DOI":"10.1016\/j.cell.2025.01.002"},{"key":"4293_CR22","doi-asserted-by":"publisher","first-page":"1320","DOI":"10.1126\/science.1253451","volume":"346","author":"ED Jarvis","year":"2014","unstructured":"Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346:1320\u201331. https:\/\/doi.org\/10.1126\/science.1253451.","journal-title":"Science"},{"key":"4293_CR23","doi-asserted-by":"publisher","unstructured":"Cicconardi F, Milanetti E, Pinheiro de Castro EC, Mazo-Vargas A, Van Belleghem SM, Ruggieri AA, et al. Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies. Nat Commun. 2023;14:5620. https:\/\/doi.org\/10.1038\/s41467-023-41412-5. Nature Publishing Group. Cited 2026 Jan 14.","DOI":"10.1038\/s41467-023-41412-5"},{"key":"4293_CR24","doi-asserted-by":"crossref","unstructured":"Bista I, McCarthy SA, Wood J, Ning Z, Detrich Iii HW, Desvignes T, et al. The genome sequence of the channel bull blenny, Cottoperca gobio (G\u00fcnther, 1861). Wellcome open research. 2020;5:148. https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC7649722\/. Cited 2025 Aug 25.","DOI":"10.12688\/wellcomeopenres.16012.1"},{"key":"4293_CR25","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1017\/S0954102000000390","volume":"12","author":"E Pisano","year":"2000","unstructured":"Pisano E, Ozouf-Costaz C. Chromosome change and the evolution in the Antarctic fish suborder Notothenioidei. Antarct Sci. 2000;12:334\u201342. https:\/\/doi.org\/10.1017\/S0954102000000390.","journal-title":"Antarct Sci"},{"key":"4293_CR26","doi-asserted-by":"publisher","unstructured":"Kapitonov VV, Tempel S, Jurka J. Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene. 2009;448:207\u201313. https:\/\/doi.org\/10.1016\/j.gene.2009.07.019. Cited 2026 Jan 14.","DOI":"10.1016\/j.gene.2009.07.019"},{"key":"4293_CR27","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.margen.2009.03.006","volume":"2","author":"E Pisano","year":"2009","unstructured":"Pisano E, Ghigliotti L. Ribosomal genes in notothenioid fishes: Focus on the chromosomal organisation. Mar Genomics. 2009;2:75\u201380. https:\/\/doi.org\/10.1016\/j.margen.2009.03.006.","journal-title":"Mar Genomics"},{"key":"4293_CR28","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1007\/978-88-470-2157-0_24","volume-title":"Fishes of Antarctica: a biological overview","author":"E Pisano","year":"1998","unstructured":"Pisano E, Ozouf-Costaz C, Prirodina V. Chromosome diversification in Antarctic fish (Notothenioidei). In: Di Prisco G, Pisano E, Clarke A, editors. Fishes of Antarctica: a biological overview. Milano: Springer Milan; 1998. p. 275\u201385. https:\/\/doi.org\/10.1007\/978-88-470-2157-0_24."},{"key":"4293_CR29","doi-asserted-by":"publisher","unstructured":"Miller KG, Browning JV, Schmelz WJ, Kopp RE, Mountain GS, Wright JD. Cenozoic sea-level and cryospheric evolution from deep-sea geochemical and continental margin records. Sci Adv. 2020;6:eaaz1346. https:\/\/doi.org\/10.1126\/sciadv.aaz1346. American Association for the Advancement of Science. Cited 2026 Jan 14.","DOI":"10.1126\/sciadv.aaz1346"},{"key":"4293_CR30","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1007\/s00300-001-0327-x","volume":"25","author":"A Stankovic","year":"2002","unstructured":"Stankovic A, Spalik K, Kamler E, Borsuk P, Weglenski P. Recent origin of sub-Antarctic notothenioids. Polar Biol. 2002;25:203\u20135. https:\/\/doi.org\/10.1007\/s00300-001-0327-x.","journal-title":"Polar Biol"},{"key":"4293_CR31","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/B978-0-12-381015-1.00004-6","volume-title":"Advances in marine biology","author":"M Collins","year":"2010","unstructured":"Collins M, Brickle P, Brown J, Belchier M. The Patagonian toothfish: biology, ecology and fishery. In: Advances in marine biology. Academic Press; 2010. p. 227\u2013300. https:\/\/doi.org\/10.1016\/B978-0-12-381015-1.00004-6."},{"key":"4293_CR32","doi-asserted-by":"publisher","unstructured":"Near TJ, Dornburg A, Harrington RC, Oliveira C, Pietsch TW, Thacker CE, et al. Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation. BMC Evol Biol. 2015;15:109. https:\/\/doi.org\/10.1186\/s12862-015-0362-9. Cited 2026 Jan 14.","DOI":"10.1186\/s12862-015-0362-9"},{"key":"4293_CR33","doi-asserted-by":"publisher","unstructured":"Detrich HW, Parker SK, Williams RC, Nogales E, Downing KH. Cold Adaptation of Microtubule Assembly and Dynamics: structural interpretation of primary sequence changes present in the \u03b1- and \u03b2-tubulins of antarctic fishes *. J Biol Chem. 2000;275:37038\u201347. https:\/\/doi.org\/10.1074\/jbc.M005699200. Elsevier. Cited 2026 Jan 14.","DOI":"10.1074\/jbc.M005699200"},{"key":"4293_CR34","doi-asserted-by":"publisher","unstructured":"Kowalczyk A, Chikina M, Clark NL. A cautionary tale on proper use of branch-site models to detect convergent positive selection. bioRxiv; 2021. p. 2021.10.26.465984. https:\/\/doi.org\/10.1101\/2021.10.26.465984. Cited 2026 Feb 5.","DOI":"10.1101\/2021.10.26.465984"},{"key":"4293_CR35","doi-asserted-by":"publisher","unstructured":"Rayamajhi N, Rivera-Col\u00f3n AG, Minhas BF, Cheng CHC, Catchen JM. The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki. G3 Genes|Genomes|Genetics. 2025;15:jkae267. https:\/\/doi.org\/10.1093\/g3journal\/jkae267. Cited 2026 Jan 14.","DOI":"10.1093\/g3journal\/jkae267"},{"key":"4293_CR36","doi-asserted-by":"publisher","unstructured":"Li H, Durbin R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet. 2024;25:658\u201370. https:\/\/doi.org\/10.1038\/s41576-024-00718-w. Nature Publishing Group. Cited 2026 July 30.","DOI":"10.1038\/s41576-024-00718-w"},{"key":"4293_CR37","doi-asserted-by":"publisher","unstructured":"Liu S, Shi C, Chen C, Tan Y, Tian Y, Macqueen DJ, et al. Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves. Cell Rep. 2025;44:115697. https:\/\/doi.org\/10.1016\/j.celrep.2025.115697. Cited 2026 Jan 14.","DOI":"10.1016\/j.celrep.2025.115697"},{"key":"4293_CR38","doi-asserted-by":"publisher","unstructured":"Rosani U, Gerdol M, Krupovic M. The highly dynamic pangenome of basal chordates is enriched in defence and immunity genes and is inherited following the Mendelian law. PLOS Genetics. 2025;21:e1011833. https:\/\/doi.org\/10.1371\/journal.pgen.1011833. Public Library of Science. Cited 2026 Feb 5.","DOI":"10.1371\/journal.pgen.1011833"},{"key":"4293_CR39","doi-asserted-by":"publisher","unstructured":"Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, et al. Characterizing the Major Structural Variant Alleles of the Human Genome. Cell. 2019;176:663\u2013675.e19. https:\/\/doi.org\/10.1016\/j.cell.2018.12.019. Elsevier. Cited 2026 Jan 14.","DOI":"10.1016\/j.cell.2018.12.019"},{"key":"4293_CR40","doi-asserted-by":"publisher","unstructured":"Chang N-C, Rovira Q, Wells J, Feschotte C, Vaquerizas JM. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression. Genome Res. 2022;32:1408\u201323. https:\/\/doi.org\/10.1101\/gr.275655.121. Cold Spring Harbor Lab. Cited 2026 Jan 14.","DOI":"10.1101\/gr.275655.121"},{"key":"4293_CR41","doi-asserted-by":"publisher","unstructured":"Lu Y, Li W, Li Y, Zhai W, Zhou X, Wu Z, et al. Population genomics of an icefish reveals mechanisms of glacier-driven adaptive radiation in Antarctic notothenioids. BMC Biol. 2022;20:231. https:\/\/doi.org\/10.1186\/s12915-022-01432-x. Cited 2026 July 30.","DOI":"10.1186\/s12915-022-01432-x"},{"key":"4293_CR42","doi-asserted-by":"publisher","unstructured":"Cao L, Huang Q, Wu Z, Cao D, Ma Z, Xu Q, et al. Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids. Nat Commun. 2016;7:12987. https:\/\/doi.org\/10.1038\/ncomms12987. Nature Publishing Group. Cited 2026 July 30.","DOI":"10.1038\/ncomms12987"},{"key":"4293_CR43","doi-asserted-by":"publisher","unstructured":"Nishiguchi T, Ishikawa A. Convergent Gene Duplication in Arctic and Antarctic Teleost Fishes. jzoo. 2025;42:116\u201326. https:\/\/doi.org\/10.2108\/zs240098. Zoological Society of Japan. Cited 2026 July 30.","DOI":"10.2108\/zs240098"},{"key":"4293_CR44","doi-asserted-by":"publisher","unstructured":"Han S, Dias GB, Basting PJ, Viswanatha R, Perrimon N, Bergman CM. Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line. Nucleic Acids Res. 2022;50:e124. https:\/\/doi.org\/10.1093\/nar\/gkac794. Cited 2026 Jan 14.","DOI":"10.1093\/nar\/gkac794"},{"key":"4293_CR45","doi-asserted-by":"publisher","first-page":"3485","DOI":"10.1093\/gbe\/evw247","volume":"8","author":"S Boissinot","year":"2016","unstructured":"Boissinot S, Sookdeo A. The evolution of LINE-1 in vertebrates. Genome Biol Evol. 2016;8:3485\u2013507. https:\/\/doi.org\/10.1093\/gbe\/evw247.","journal-title":"Genome Biol Evol"},{"key":"4293_CR46","doi-asserted-by":"publisher","unstructured":"Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol. 2023;21:145. https:\/\/doi.org\/10.1186\/s12915-023-01632-z. Cited 2026 Jan 14.","DOI":"10.1186\/s12915-023-01632-z"},{"key":"4293_CR47","doi-asserted-by":"publisher","unstructured":"Davis KE, Hill J, Astrop TI, Wills MA. Global cooling as a driver of diversification in a major marine clade. Nat Commun. 2016;7:13003. https:\/\/doi.org\/10.1038\/ncomms13003. Nature Publishing Group. Cited 2026 Jan 14.","DOI":"10.1038\/ncomms13003"},{"key":"4293_CR48","doi-asserted-by":"publisher","unstructured":"Ch\u00e9nais B, Caruso A, Hiard S, Casse N. The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments. Gene. 2012;509:7\u201315. https:\/\/doi.org\/10.1016\/j.gene.2012.07.042. Cited 2026 Jan 14.","DOI":"10.1016\/j.gene.2012.07.042"},{"key":"4293_CR49","doi-asserted-by":"publisher","unstructured":"Chen S, Yu M, Chu X, Li W, Yin X, Chen L. Cold-induced retrotransposition of fish LINEs. J Genet Genom. 2017;44:385\u201394. https:\/\/doi.org\/10.1016\/j.jgg.2017.07.002. Cited 2026 Jan 14.","DOI":"10.1016\/j.jgg.2017.07.002"},{"key":"4293_CR50","doi-asserted-by":"publisher","unstructured":"Amores A, Wilson CA, Allard CAH, Detrich HW III, Postlethwait JH. Cold Fusion: Massive Karyotype Evolution in the Antarctic Bullhead Notothen Notothenia coriiceps. G3 Genes|Genomes|Genetics. 2017;7:2195\u2013207. https:\/\/doi.org\/10.1534\/g3.117.040063. Cited 2026 Mar 9.","DOI":"10.1534\/g3.117.040063"},{"key":"4293_CR51","doi-asserted-by":"publisher","unstructured":"Gerton JL. A working model for the formation of Robertsonian chromosomes. J Cell Sci. 2024;137:jcs261912. https:\/\/doi.org\/10.1242\/jcs.261912. Cited 2026 Jan 11.","DOI":"10.1242\/jcs.261912"},{"key":"4293_CR52","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1093\/nar\/gkh280","volume":"32","author":"LR Read","year":"2004","unstructured":"Read LR, Raynard SJ, Ruk\u015b\u0107 A, Baker MD. Gene repeat expansion and contraction by spontaneous intrachromosomal homologous recombination in mammalian cells. Nucleic Acids Res. 2004;32:1184\u201396. https:\/\/doi.org\/10.1093\/nar\/gkh280.","journal-title":"Nucleic Acids Res"},{"key":"4293_CR53","doi-asserted-by":"publisher","unstructured":"Raymond JA, DeVries AL. Adsorption inhibition as a mechanism of freezing resistance in polar fishes. Proc Natl Acad Sci. 1977;74:2589\u201393. https:\/\/doi.org\/10.1073\/pnas.74.6.2589. Cited 2026 Jan 21.","DOI":"10.1073\/pnas.74.6.2589"},{"key":"4293_CR54","doi-asserted-by":"publisher","unstructured":"DeVries AL. The role of antifreeze glycopeptides and peptides in the freezing avoidance of Antarctic fishes. Compar Biochem Physiol Part B Compar Biochem. 1988;90:611\u201321. https:\/\/doi.org\/10.1016\/0305-0491(88)90302-1. Cited 2026 Jan 21.","DOI":"10.1016\/0305-0491(88)90302-1"},{"key":"4293_CR55","doi-asserted-by":"publisher","unstructured":"Schrag JD, Devries AL. The effect of freezing rate on the cooperativity of antifreeze glycopeptides. Compar Biochem Physiol Part A Physiol. 1983;74:381\u20135. https:\/\/doi.org\/10.1016\/0300-9629(83)90619-9. Cited 2026 Jan 21.","DOI":"10.1016\/0300-9629(83)90619-9"},{"key":"4293_CR56","doi-asserted-by":"publisher","unstructured":"Frandsen PB, Hotaling S, Powell A, Heckenhauer J, Kawahara AY, Baker RH, et al. Allelic resolution of insect and spider silk genes reveals hidden genetic diversity. Proc Natl Acad Sci. 2023;120:e2221528120. https:\/\/doi.org\/10.1073\/pnas.2221528120. Cited 2026 Jan 14.","DOI":"10.1073\/pnas.2221528120"},{"key":"4293_CR57","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abo6043","volume":"8","author":"K Arakawa","year":"2022","unstructured":"Arakawa K, Kono N, Malay AD, Tateishi A, Ifuku N, Masunaga H, et al. 1000 spider silkomes: linking sequences to silk physical properties. Sci Adv. 2022;8:eabo6043. https:\/\/doi.org\/10.1126\/sciadv.abo6043.","journal-title":"Sci Adv"},{"key":"4293_CR58","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1017\/S0954102015000413","volume":"28","author":"T Miya","year":"2016","unstructured":"Miya T, Gon O, Mwale M, Cheng C-HC. Multiple independent reduction or loss of antifreeze trait in low Antarctic and sub-Antarctic notothenioid fishes. Antarct Sci. 2016;28:17\u201328. https:\/\/doi.org\/10.1017\/S0954102015000413.","journal-title":"Antarct Sci"},{"key":"4293_CR59","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1016\/j.cbpb.2004.05.013","volume":"138","author":"D Abele","year":"2004","unstructured":"Abele D, Puntarulo S. Formation of reactive species and induction of antioxidant defence systems in polar and temperate marine invertebrates and fish. Comp Biochem Physiol A Mol Integr Physiol. 2004;138:405\u201315. https:\/\/doi.org\/10.1016\/j.cbpb.2004.05.013.","journal-title":"Comp Biochem Physiol A Mol Integr Physiol"},{"key":"4293_CR60","doi-asserted-by":"publisher","unstructured":"Peck LS. A Cold Limit to Adaptation in the Sea. Trends Ecol Evol. 2016;31:13\u201326. https:\/\/doi.org\/10.1016\/j.tree.2015.09.014. Elsevier. Cited 2026 Jan 11.","DOI":"10.1016\/j.tree.2015.09.014"},{"key":"4293_CR61","doi-asserted-by":"publisher","unstructured":"Carpenter JH. New Measurements of Oxygen Solubility in Pure and Natural Water. Limnol Oceanography. 1966;11:264\u201377. https:\/\/doi.org\/10.4319\/lo.1966.11.2.0264. Cited 2026 Jan 11.","DOI":"10.4319\/lo.1966.11.2.0264"},{"key":"4293_CR62","doi-asserted-by":"publisher","unstructured":"Olmos Y, S\u00e1nchez-G\u00f3mez FJ, Wild B, Garc\u00eda-Quintans N, Cabezudo S, Lamas S, et al. SirT1 Regulation of Antioxidant Genes Is Dependent on the Formation of a FoxO3a\/PGC-1\u03b1 Complex. Antioxidants Redox Signal. 2013;19:1507\u201321. https:\/\/doi.org\/10.1089\/ars.2012.4713. Mary Ann Liebert, Inc., publishers. Cited 2026 Jan 14.","DOI":"10.1089\/ars.2012.4713"},{"key":"4293_CR63","doi-asserted-by":"publisher","unstructured":"Ferko M, Alanova P, Janko D, Opletalova B, Andelova N. Mitochondrial Peroxiredoxins and Monoamine Oxidase-A: Dynamic Regulators of ROS Signaling in Cardioprotection. Physiol Res. 2024;73:887\u2013900. https:\/\/doi.org\/10.33549\/physiolres.935513. Cited 2026 Jan 14.","DOI":"10.33549\/physiolres.935513"},{"key":"4293_CR64","doi-asserted-by":"publisher","unstructured":"Bilyk KT, Zhuang X, Papetti C. Positive and Relaxed Selective Pressures Have Both Strongly Influenced the Evolution of Cryonotothenioid Fishes during Their Radiation in the Freezing Southern Ocean. Genome Biol Evol. 2023;15:evad049. https:\/\/doi.org\/10.1093\/gbe\/evad049. Cited 2026 Jan 23.","DOI":"10.1093\/gbe\/evad049"},{"key":"4293_CR65","doi-asserted-by":"publisher","unstructured":"Shin SC, Ahn DH, Kim SJ, Pyo CW, Lee H, Kim M-K, et al. The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. Genome Biol. 2014;15:468. https:\/\/doi.org\/10.1186\/s13059-014-0468-1. Cited 2026 Jan 14.","DOI":"10.1186\/s13059-014-0468-1"},{"key":"4293_CR66","doi-asserted-by":"publisher","unstructured":"Chen Z, Cheng C-HC, Zhang J, Cao L, Chen L, Zhou L, et al. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc Natl Acad Sci. 2008;105:12944\u20139. https:\/\/doi.org\/10.1073\/pnas.0802432105. Cited 2025 Nov 19.","DOI":"10.1073\/pnas.0802432105"},{"key":"4293_CR67","doi-asserted-by":"publisher","unstructured":"Clark MS, Thorne MAS, Toullec J-Y, Meng Y, Guan LL, Peck LS, et al. Antarctic Krill 454 Pyrosequencing Reveals Chaperone and Stress Transcriptome. PLOS ONE. 2011;6:e15919. https:\/\/doi.org\/10.1371\/journal.pone.0015919. Public Library of Science. Cited 2026 Jan 11.","DOI":"10.1371\/journal.pone.0015919"},{"key":"4293_CR68","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1017\/S0954102001000189","volume":"13","author":"D Abele","year":"2001","unstructured":"Abele D, Tesch C, Wencke P, P\u00f6rtner HO. How does oxidative stress relate to thermal tolerance in the Antarctic bivalve Yoldia eightsi? Antarct Sci. 2001;13:111\u20138. https:\/\/doi.org\/10.1017\/S0954102001000189.","journal-title":"Antarct Sci"},{"key":"4293_CR69","doi-asserted-by":"publisher","unstructured":"Fraser KPP, Rogers AD. Protein Metabolism in Marine Animals: The Underlying Mechanism of Growth. Adv Marine Biol. 2007. p. 267\u2013362. https:\/\/doi.org\/10.1016\/S0065-2881(06)52003-6. Academic Press. Cited 2026 Jan 11.","DOI":"10.1016\/S0065-2881(06)52003-6"},{"key":"4293_CR70","doi-asserted-by":"publisher","unstructured":"Todgham AE, Hoaglund EA, Hofmann GE. Is cold the new hot? Elevated ubiquitin-conjugated protein levels in tissues of Antarctic fish as evidence for cold-denaturation of proteins in vivo. J Comp Physiol B. 2007;177:857\u201366. https:\/\/doi.org\/10.1007\/s00360-007-0183-2. Cited 2026 Jan 11.","DOI":"10.1007\/s00360-007-0183-2"},{"key":"4293_CR71","doi-asserted-by":"publisher","unstructured":"Hofmann GE, Lund SG, Place SP, Whitmer AC. Some like it hot, some like it cold: the heat shock response is found in New Zealand but not Antarctic notothenioid fishes. J Exp Marine Biol Ecol. 2005;316:79\u201389. https:\/\/doi.org\/10.1016\/j.jembe.2004.10.007. Cited 2026 Jan 11.","DOI":"10.1016\/j.jembe.2004.10.007"},{"key":"4293_CR72","doi-asserted-by":"publisher","DOI":"10.1152\/ajpregu.00223.2004","author":"SP Place","year":"2004","unstructured":"Place SP, Zippay ML, Hofmann GE. Constitutive roles for inducible genes: evidence for the alteration in expression of the inducible hsp70 gene in Antarctic notothenioid fishes. Am J Physiol Regul Integr Comp Physiol. 2004. https:\/\/doi.org\/10.1152\/ajpregu.00223.2004.","journal-title":"Am J Physiol Regul Integr Comp Physiol"},{"key":"4293_CR73","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1242\/jeb.145946","volume":"220","author":"AE Todgham","year":"2017","unstructured":"Todgham AE, Crombie TA, Hofmann GE. The effect of temperature adaptation on the ubiquitin\u2013proteasome pathway in notothenioid fishes. J Exp Biol. 2017;220:369\u201378. https:\/\/doi.org\/10.1242\/jeb.145946.","journal-title":"J Exp Biol"},{"key":"4293_CR74","doi-asserted-by":"crossref","unstructured":"Strickland M, Moll R, Cornwell C, Smith M, Howard C. Sanger Tree of Life HMW DNA Extraction: Manual MagAttract. 2023. https:\/\/www.protocols.io\/view\/sanger-tree-of-life-hmw-dna-extraction-manual-maga-cy3ixyke. Cited 2026 Feb 16.","DOI":"10.17504\/protocols.io.6qpvr33novmk\/v1"},{"key":"4293_CR75","doi-asserted-by":"publisher","unstructured":"Cheng H, Concepcion GT, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18:170\u20135. https:\/\/doi.org\/10.1038\/s41592-020-01056-5. Nature Publishing Group. Cited 2026 Jan 15.","DOI":"10.1038\/s41592-020-01056-5"},{"key":"4293_CR76","doi-asserted-by":"publisher","unstructured":"Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). 2019. p. 314\u201324. https:\/\/doi.org\/10.1109\/IPDPS.2019.00041. Cited 2026 Jan 15.","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"4293_CR77","doi-asserted-by":"publisher","unstructured":"Zhou C, McCarthy SA, Durbin R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39:btac808. https:\/\/doi.org\/10.1093\/bioinformatics\/btac808. Cited 2026 Jan 14.","DOI":"10.1093\/bioinformatics\/btac808"},{"key":"4293_CR78","doi-asserted-by":"publisher","unstructured":"Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA. 2020;117:9451\u20137. https:\/\/doi.org\/10.1073\/pnas.1921046117. Cited 2025 Dec 9.","DOI":"10.1073\/pnas.1921046117"},{"key":"4293_CR79","doi-asserted-by":"publisher","unstructured":"Orozco-Arias S, Sierra P, Durbin R, Gonz\u00e1lez J. MCHelper automatically curates transposable element libraries across eukaryotic species. Genome Res. 2024;34:2256\u201368. https:\/\/doi.org\/10.1101\/gr.278821.123. Cold Spring Harbor Laboratory Press. Cited 2026 July 30.","DOI":"10.1101\/gr.278821.123"},{"key":"4293_CR80","doi-asserted-by":"publisher","unstructured":"Lin Y, Ye C, Li X, Chen Q, Wu Y, Zhang F, et al. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic Res. 2023;10:uhad127. https:\/\/doi.org\/10.1093\/hr\/uhad127. Cited 2026 Feb 5.","DOI":"10.1093\/hr\/uhad127"},{"key":"4293_CR81","unstructured":"Seemann T. tseemann\/barrnap. 2026. https:\/\/github.com\/tseemann\/barrnap. Cited 2026 Mar 5."},{"key":"4293_CR82","doi-asserted-by":"publisher","unstructured":"Brown MR, Manuel Gonzalez de La Rosa P, Blaxter M. tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. Bioinformatics. 2025;41:btaf049. https:\/\/doi.org\/10.1093\/bioinformatics\/btaf049. Cited 2026 Jan 14.","DOI":"10.1093\/bioinformatics\/btaf049"},{"key":"4293_CR83","doi-asserted-by":"publisher","unstructured":"Gabriel L, Br\u016fna T, Hoff KJ, Ebel M, Lomsadze A, Borodovsky M, et al. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA. Genome Res. 2024;34:769\u201377. https:\/\/doi.org\/10.1101\/gr.278090.123. Cold Spring Harbor Lab. Cited 2026 Jan 14.","DOI":"10.1101\/gr.278090.123"},{"key":"4293_CR84","doi-asserted-by":"publisher","unstructured":"Hoff KJ, Stanke M. Predicting Genes in Single Genomes with AUGUSTUS. Current Protocols in Bioinformatics. 2019;65:e57. https:\/\/doi.org\/10.1002\/cpbi.57. Cited 2026 Jan 14.","DOI":"10.1002\/cpbi.57"},{"key":"4293_CR85","doi-asserted-by":"publisher","unstructured":"Br\u016fna T, Lomsadze A, Borodovsky M. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genom Bioinform. 2020;2:lqaa026. https:\/\/doi.org\/10.1093\/nargab\/lqaa026. Cited 2026 Jan 14.","DOI":"10.1093\/nargab\/lqaa026"},{"key":"4293_CR86","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907\u201315. https:\/\/doi.org\/10.1038\/s41587-019-0201-4.","journal-title":"Nat Biotechnol"},{"key":"4293_CR87","doi-asserted-by":"publisher","unstructured":"Manni M, Berkeley MR, Seppey M, Sim\u00e3o FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021;38:4647\u201354. https:\/\/doi.org\/10.1093\/molbev\/msab199. Cited 2026 Jan 14.","DOI":"10.1093\/molbev\/msab199"},{"key":"4293_CR88","doi-asserted-by":"publisher","unstructured":"Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics. 2021;37:1639\u201343. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa1016. Cited 2026 Jan 14.","DOI":"10.1093\/bioinformatics\/btaa1016"},{"key":"4293_CR89","doi-asserted-by":"publisher","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021;38:5825\u20139. https:\/\/doi.org\/10.1093\/molbev\/msab293. Cited 2026 Jan 14.","DOI":"10.1093\/molbev\/msab293"},{"key":"4293_CR90","doi-asserted-by":"publisher","unstructured":"Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236\u201340. https:\/\/doi.org\/10.1093\/bioinformatics\/btu031. Cited 2026 July 30.","DOI":"10.1093\/bioinformatics\/btu031"},{"key":"4293_CR91","doi-asserted-by":"publisher","unstructured":"Li H. Protein-to-genome alignment with miniprot. Bioinformatics. 2023;39:btad014. https:\/\/doi.org\/10.1093\/bioinformatics\/btad014. Cited 2026 July 30.","DOI":"10.1093\/bioinformatics\/btad014"},{"key":"4293_CR92","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1007\/978-1-4939-9173-0_9","volume-title":"Gene prediction: methods and protocols","author":"J Keilwagen","year":"2019","unstructured":"Keilwagen J, Hartung F, Grau J. GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data. In: Kollmar M, editor. Gene prediction: methods and protocols. New York, NY: Springer; 2019. p. 161\u201377. https:\/\/doi.org\/10.1007\/978-1-4939-9173-0_9."},{"key":"4293_CR93","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403\u201310. https:\/\/doi.org\/10.1016\/S0022-2836(05)80360-2.","journal-title":"J Mol Biol"},{"key":"4293_CR94","doi-asserted-by":"publisher","unstructured":"Madrigal G, Minhas BF, Catchen J. Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs. Mol Ecol Res. 2025;25:e13982. https:\/\/doi.org\/10.1111\/1755-0998.13982. Cited 2026 Jan 14.","DOI":"10.1111\/1755-0998.13982"},{"key":"4293_CR95","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772\u201380. https:\/\/doi.org\/10.1093\/molbev\/mst010.","journal-title":"Mol Biol Evol"},{"key":"4293_CR96","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530\u20134. https:\/\/doi.org\/10.1093\/molbev\/msaa015.","journal-title":"Mol Biol Evol"},{"key":"4293_CR97","doi-asserted-by":"publisher","unstructured":"Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol. 2018;35:518\u201322. https:\/\/doi.org\/10.1093\/molbev\/msx281. Cited 2026 Jan 14.","DOI":"10.1093\/molbev\/msx281"},{"key":"4293_CR98","doi-asserted-by":"publisher","unstructured":"Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587\u20139. https:\/\/doi.org\/10.1038\/nmeth.4285. Nature Publishing Group. Cited 2026 Jan 14.","DOI":"10.1038\/nmeth.4285"},{"key":"4293_CR99","doi-asserted-by":"publisher","unstructured":"Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49:D412\u20139. https:\/\/doi.org\/10.1093\/nar\/gkaa913. Cited 2026 Jan 15.","DOI":"10.1093\/nar\/gkaa913"},{"key":"4293_CR100","doi-asserted-by":"publisher","unstructured":"Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/bts565. Cited 2026 Jan 15.","DOI":"10.1093\/bioinformatics\/bts565"},{"key":"4293_CR101","doi-asserted-by":"publisher","unstructured":"Capella-Guti\u00e9rrez S, Silla-Mart\u00ednez JM, Gabald\u00f3n T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btp348. Cited 2026 Jan 14.","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"4293_CR102","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1093\/gbe\/evw009","volume":"8","author":"RN Platt II","year":"2016","unstructured":"Platt RN II, Blanco-Berdugo L, Ray DA. Accurate transposable element annotation is vital when analyzing new genome assemblies. Genome Biol Evol. 2016;8:403\u201310. https:\/\/doi.org\/10.1093\/gbe\/evw009.","journal-title":"Genome Biol Evol"},{"key":"4293_CR103","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-021-00259-7","volume":"13","author":"C Goubert","year":"2022","unstructured":"Goubert C, Craig RJ, Bilat AF, Peona V, Vogan AA, Protasio AV. A beginner\u2019s guide to manual curation of transposable elements. Mob DNA. 2022;13:7. https:\/\/doi.org\/10.1186\/s13100-021-00259-7.","journal-title":"Mob DNA"},{"key":"4293_CR104","doi-asserted-by":"publisher","unstructured":"Peona V, Martelossi J, Almojil D, Bocharkina J, Br\u00e4nnstr\u00f6m I, Brown M, et al. Teaching transposon classification as a means to crowd source the curation of repeat annotation \u2013 a tardigrade perspective. Mobile DNA. 2024;15:10. https:\/\/doi.org\/10.1186\/s13100-024-00319-8. Cited 2026 Jan 15.","DOI":"10.1186\/s13100-024-00319-8"},{"key":"4293_CR105","doi-asserted-by":"publisher","unstructured":"Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094\u2013100. https:\/\/doi.org\/10.1093\/bioinformatics\/bty191.Cited 2025 Oct 27.","DOI":"10.1093\/bioinformatics\/bty191."},{"key":"4293_CR106","doi-asserted-by":"publisher","unstructured":"Goel M, Sun H, Jiao W-B, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019;20:277. https:\/\/doi.org\/10.1186\/s13059-019-1911-0. Cited 2026 Jan 14.","DOI":"10.1186\/s13059-019-1911-0"},{"key":"4293_CR107","doi-asserted-by":"publisher","unstructured":"Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btq033. Cited 2026 Jan 14.","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"4293_CR108","doi-asserted-by":"publisher","unstructured":"Bates D, M\u00e4chler M, Bolker B, Walker S. Fitting Linear Mixed-Effects Models Using lme4. J Stat Software. 2015;67:1\u201348. https:\/\/doi.org\/10.18637\/jss.v067.i01. Cited 2026 Jan 14.","DOI":"10.18637\/jss.v067.i01"},{"key":"4293_CR109","doi-asserted-by":"publisher","unstructured":"Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024;42:1571\u201380. https:\/\/doi.org\/10.1038\/s41587-023-02024-y. Nature Publishing Group. Cited 2026 Jan 14.","DOI":"10.1038\/s41587-023-02024-y"},{"key":"4293_CR110","doi-asserted-by":"publisher","unstructured":"Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017;8:14061. https:\/\/doi.org\/10.1038\/ncomms14061. Nature Publishing Group. Cited 2026 Jan 14.","DOI":"10.1038\/ncomms14061"},{"key":"4293_CR111","doi-asserted-by":"publisher","unstructured":"Bista I, Collins M. The genome sequence of the marbled rockcod, Notothenia rossii Richardson, 1844. Wellcome Open Res. 2024;9:227. https:\/\/doi.org\/10.12688\/wellcomeopenres.21270.1. Cited 2025 Nov 15.","DOI":"10.12688\/wellcomeopenres.21270.1"},{"key":"4293_CR112","doi-asserted-by":"publisher","unstructured":"Cheng C-HC, Rivera-Col\u00f3n AG, Minhas BF, Wilson L, Rayamajhi N, Vargas-Chacoff L, et al. Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes. 2023;14:1196. https:\/\/doi.org\/10.3390\/genes14061196. Multidisciplinary Digital Publishing Institute. Cited 2026 Jan 15.","DOI":"10.3390\/genes14061196"},{"key":"4293_CR113","doi-asserted-by":"publisher","unstructured":"Jae Lee S, Kim J-H, Jo E, Choi E, Kim J, Choi S-G, et al. Chromosomal assembly of the Antarctic toothfish (Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. Zool Res. 2021;42:124\u20139. https:\/\/doi.org\/10.24272\/j.issn.2095-8137.2020.264. Cited 2026 Jan 15.","DOI":"10.24272\/j.issn.2095-8137.2020.264"},{"key":"4293_CR114","doi-asserted-by":"publisher","unstructured":"Lee SJ, Kim J, Choi EK, Jo E, Cho M, Kim J-H, et al. A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus. Sci Data. 2023;10:657. https:\/\/doi.org\/10.1038\/s41597-023-02561-w. Nature Publishing Group. Cited 2026 Jan 15.","DOI":"10.1038\/s41597-023-02561-w"},{"key":"4293_CR115","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkae267","volume":"15","author":"N Rayamajhi","year":"2025","unstructured":"Rayamajhi N, Rivera-Col\u00f3n AG, Minhas BF, Cheng CHC, Catchen JM. The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki. G3 (Bethesda). 2025;15:jkae267. https:\/\/doi.org\/10.1093\/g3journal\/jkae267.","journal-title":"G3 (Bethesda)"},{"key":"4293_CR116","doi-asserted-by":"publisher","unstructured":"Jo E, Choi S, Lee SJ, Kim J, Choi EK, Cho M, et al. Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna. Sci Data. 2023;10:891. https:\/\/doi.org\/10.1038\/s41597-023-02811-x. Nature Publishing Group. Cited 2026 Jan 15.","DOI":"10.1038\/s41597-023-02811-x"},{"key":"4293_CR117","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1093\/sysbio\/syv068","volume":"65","author":"T-H To","year":"2016","unstructured":"To T-H, Jung M, Lycett S, Gascuel O. Fast dating using least-squares criteria and algorithms. Syst Biol. 2016;65:82\u201397. https:\/\/doi.org\/10.1093\/sysbio\/syv068.","journal-title":"Syst Biol"},{"issue":"1","key":"4293_CR118","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):238. https:\/\/doi.org\/10.1186\/s13059-019-1832-y.","journal-title":"Genome Biol"},{"key":"4293_CR119","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1093\/sysbio\/syab070","volume":"71","author":"J Willson","year":"2022","unstructured":"Willson J, Roddur MS, Liu B, Zaharias P, Warnow T. DISCO: species tree inference using multicopy gene family tree decomposition. Syst Biol. 2022;71:610\u201329. https:\/\/doi.org\/10.1093\/sysbio\/syab070.","journal-title":"Syst Biol"},{"key":"4293_CR120","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1007\/978-1-62703-646-7_10","volume-title":"Multiple sequence alignment methods","author":"A L\u00f6ytynoja","year":"2014","unstructured":"L\u00f6ytynoja A. Phylogeny-aware alignment with PRANK. In: Russell DJ, editor. Multiple sequence alignment methods. Totowa, NJ: Humana Press; 2014. p. 155\u201370. https:\/\/doi.org\/10.1007\/978-1-62703-646-7_10."},{"key":"4293_CR121","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1080\/10635150701472164","volume":"56","author":"G Talavera","year":"2007","unstructured":"Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56:564\u201377. https:\/\/doi.org\/10.1080\/10635150701472164.","journal-title":"Syst Biol"},{"key":"4293_CR122","doi-asserted-by":"publisher","unstructured":"Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection. Mol Biol Evol. 2015;32:1342\u201353. https:\/\/doi.org\/10.1093\/molbev\/msv022. Cited 2026 Jan 15.","DOI":"10.1093\/molbev\/msv022"},{"key":"4293_CR123","unstructured":"Alexa A, Rahnenf\u00fchrer J, Marini F. topGO. Bioconductor. http:\/\/bioconductor.org\/packages\/topGO\/. Cited 2026 Jan 15."},{"key":"4293_CR124","doi-asserted-by":"publisher","unstructured":"Lovell JT, Sreedasyam A, Schranz ME, Wilson M, Carlson JW, Harkess A, et al. GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. Weigel D, editor. eLife. 2022;11:e78526. https:\/\/doi.org\/10.7554\/eLife.78526. eLife Sciences Publications, Ltd. Cited 2026 Jan 15.","DOI":"10.7554\/eLife.78526"},{"key":"4293_CR125","doi-asserted-by":"publisher","unstructured":"Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020;587:246\u201351. https:\/\/doi.org\/10.1038\/s41586-020-2871-y. Nature Publishing Group. Cited 2026 Jan 15.","DOI":"10.1038\/s41586-020-2871-y"},{"key":"4293_CR126","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1093\/bioinformatics\/btt128","volume":"29","author":"G Hickey","year":"2013","unstructured":"Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 2013;29:1341\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btt128.","journal-title":"Bioinformatics"},{"key":"4293_CR127","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1093\/bib\/bbq072","volume":"12","author":"MJ Hubisz","year":"2011","unstructured":"Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space\/time models. Brief Bioinform. 2011;12:41\u201351. https:\/\/doi.org\/10.1093\/bib\/bbq072.","journal-title":"Brief Bioinform"},{"key":"4293_CR128","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576\u201389. https:\/\/doi.org\/10.1016\/j.molcel.2010.05.004.","journal-title":"Mol Cell"},{"key":"4293_CR129","doi-asserted-by":"crossref","unstructured":"Martelossi J, Krasheninnikova K, Denton A, Wood JMD, Mathers T, Durbin R, Fong N, Bentley DL, Clark MS, Bista I. A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation. Genome Assembly fHarAnt1, European Nucleotide Archive (ENA). 2026. https:\/\/www.ebi.ac.uk\/ena\/browser\/text-search?query=fHarAnt1.","DOI":"10.64898\/2026.04.21.719633"},{"key":"4293_CR130","doi-asserted-by":"crossref","unstructured":"Martelossi J, Krasheninnikova K, Denton A, Wood JMD, Mathers T, Durbin R, Fong N, Bentley DL, Clark MS, Bista I.\u00a0A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation. Nanopore reads for genome Assembly fHarAnt1.2, European Nucleotide Archive (ENA). 2026. https:\/\/www.ncbi.nlm.nih.gov\/sra\/ERX16667749 [accn].","DOI":"10.64898\/2026.04.21.719633"},{"key":"4293_CR131","doi-asserted-by":"publisher","unstructured":"Martelossi J, Krasheninnikova K, Denton A, Wood JMD, Mathers T, Durbin R, Fong N, Bentley DL, Clark MS, Bista I.\u00a0A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation. RNAseq data, BioStudies database. 2026. https:\/\/doi.org\/10.6019\/E-MTAB-17028.","DOI":"10.6019\/E-MTAB-17028"},{"key":"4293_CR132","doi-asserted-by":"publisher","unstructured":"Martelossi J, Krasheninnikova K, Denton A, Wood JMD, Mathers T, Durbin R, Fong N, Bentley DL, Clark MS, Bista I.\u00a0Annotations for: A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation. Zenodo. 2026. https:\/\/doi.org\/10.5281\/zenodo.21629331.","DOI":"10.5281\/zenodo.21629331"},{"key":"4293_CR133","unstructured":"Martelossi J. Check monophyly script. GitHub. 2026. https:\/\/github.com\/jacopoM28\/Check_monophyly."}],"container-title":["Genome Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13059-026-04293-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-026-04293-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-026-04293-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T17:45:14Z","timestamp":1792086314000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13059-026-04293-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,15]]},"references-count":133,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["4293"],"URL":"https:\/\/doi.org\/10.1186\/s13059-026-04293-7","relation":{},"ISSN":["1474-760X"],"issn-type":[{"value":"1474-760X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,15]]},"assertion":[{"value":"9 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All research was conducted under Antarctic Treaty permits issued by the UK Foreign, Commonwealth and Development Office to British Antarctic Survey. United Kingdom of Great Britain and Northern Ireland, Antarctic Act 1994 Antarctic Act 2013, Antarctic Regulations 1995\/490 (as amended). Permit number BAS-S7-2018\/3 granted under Section 7 of the Antarctic Act 1994. All experimental work was approved by the British Antarctic Survey Ethical Review Committee, who confirmed that no animal ethics approval was necessary.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"317"}}