Genomics of cold adaptations in the Antarctic notothenioid fish radiation
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jats:titleAbstract</jats:title>jats:pNumerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.</jats:p>
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Acknowledgements: We thank the Wellcome Sanger Institute Scientific Operations for help with sequencing data production. We thank Laura Gerrish for help with generating an ArcGIS map of Antarctica and the Southern Ocean. I.B., S.A.M., and R.D. were supported by Wellcome grants WT207492 and WT206194; I.B. and E.A.M. by Wellcome grants 104640 and 092096; C.H.C.C. by US National Science Foundation grant ANT11-42158; M.M. by a mobility fellowship from the Norwegian Research Council (FRIPRO 275869); T.D., J.H.P. by NSF OPP-1543383 and OPP-1947040; H.W.D. by US National Science Foundation grants OPP-0132032, PLR-1444167, and OPP-1955368, and the Marine Science Centre at Northeastern University (publication number 427), M.S.C. by NERC-UKRI core funding to the British Antarctic Survey; W.S. by Swiss National Science Foundation (176039). J.M.D.W., Y.S., J.T., W.C., and K.H. by Wellcome WT206194; L.H. by WT108749 and WT222155. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
Funder: US National Science Foundation grants OPP-1543383 and OPP-1947040
Funder: Norwegian Research Council(FRIPRO 275869)
Funder: Swiss National Science Foundation (176039)
Funder: RCUK | NERC | British Antarctic Survey (BAS); doi: https://doi.org/10.13039/501100007849
Funder: US National Science Foundation grants OPP-0132032, PLR-1444167, and OPP-1955368
Funder: US National Science Foundation grant ANT11-42158
