Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants
Comparative genomics studies typically limit their focus to single nucleotide variants (SNVs) and that was the case for previous comparisons of woolly mammoth genomes. We extended the analysis to systematically identify not only SNVs but also larger structural variants (SVs) and indels and found mul...
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ftpubmed:oai:pubmedcentral.nih.gov:5737375 2023-05-15T15:05:25+02:00 Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants Smith, Sean D. Kawash, Joseph K. Karaiskos, Spyros Biluck, Ian Grigoriev, Andrey 2017-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737375/ http://www.ncbi.nlm.nih.gov/pubmed/28369217 https://doi.org/10.1093/dnares/dsx007 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737375/ http://www.ncbi.nlm.nih.gov/pubmed/28369217 http://dx.doi.org/10.1093/dnares/dsx007 © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com CC-BY-NC Full Papers Text 2017 ftpubmed https://doi.org/10.1093/dnares/dsx007 2018-01-14T01:08:13Z Comparative genomics studies typically limit their focus to single nucleotide variants (SNVs) and that was the case for previous comparisons of woolly mammoth genomes. We extended the analysis to systematically identify not only SNVs but also larger structural variants (SVs) and indels and found multiple mammoth-specific deletions and duplications affecting exons or even complete genes. The most prominent SV found was an amplification of RNase L (with different copy numbers in different mammoth genomes, up to 9-fold), involved in antiviral defense and inflammasome function. This amplification was accompanied by mutations affecting several domains of the protein including the active site and produced different sets of RNase L paralogs in four mammoth genomes likely contributing to adaptations to environmental threats. In addition to immunity and defense, we found many other unique genetic changes in woolly mammoths that suggest adaptations to life in harsh Arctic conditions, including variants involving lipid metabolism, circadian rhythms, and skeletal and body features. Together, these variants paint a complex picture of evolution of the mammoth species and may be relevant in the studies of their population history and extinction. Text Arctic PubMed Central (PMC) Arctic DNA Research 24 4 359 369 |
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Full Papers Smith, Sean D. Kawash, Joseph K. Karaiskos, Spyros Biluck, Ian Grigoriev, Andrey Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
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Full Papers |
description |
Comparative genomics studies typically limit their focus to single nucleotide variants (SNVs) and that was the case for previous comparisons of woolly mammoth genomes. We extended the analysis to systematically identify not only SNVs but also larger structural variants (SVs) and indels and found multiple mammoth-specific deletions and duplications affecting exons or even complete genes. The most prominent SV found was an amplification of RNase L (with different copy numbers in different mammoth genomes, up to 9-fold), involved in antiviral defense and inflammasome function. This amplification was accompanied by mutations affecting several domains of the protein including the active site and produced different sets of RNase L paralogs in four mammoth genomes likely contributing to adaptations to environmental threats. In addition to immunity and defense, we found many other unique genetic changes in woolly mammoths that suggest adaptations to life in harsh Arctic conditions, including variants involving lipid metabolism, circadian rhythms, and skeletal and body features. Together, these variants paint a complex picture of evolution of the mammoth species and may be relevant in the studies of their population history and extinction. |
format |
Text |
author |
Smith, Sean D. Kawash, Joseph K. Karaiskos, Spyros Biluck, Ian Grigoriev, Andrey |
author_facet |
Smith, Sean D. Kawash, Joseph K. Karaiskos, Spyros Biluck, Ian Grigoriev, Andrey |
author_sort |
Smith, Sean D. |
title |
Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
title_short |
Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
title_full |
Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
title_fullStr |
Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
title_full_unstemmed |
Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
title_sort |
evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants |
publisher |
Oxford University Press |
publishDate |
2017 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737375/ http://www.ncbi.nlm.nih.gov/pubmed/28369217 https://doi.org/10.1093/dnares/dsx007 |
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Arctic |
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Arctic |
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Arctic |
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Arctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737375/ http://www.ncbi.nlm.nih.gov/pubmed/28369217 http://dx.doi.org/10.1093/dnares/dsx007 |
op_rights |
© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
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CC-BY-NC |
op_doi |
https://doi.org/10.1093/dnares/dsx007 |
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DNA Research |
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24 |
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