Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function
Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modifications, including high mitochondri...
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ftpubmed:oai:pubmedcentral.nih.gov:3595028 2023-05-15T14:05:20+02:00 Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function Coppe, Alessandro Agostini, Cecilia Marino, Ilaria A.M. Zane, Lorenzo Bargelloni, Luca Bortoluzzi, Stefania Patarnello, Tomaso 2013 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595028 http://www.ncbi.nlm.nih.gov/pubmed/23196969 https://doi.org/10.1093/gbe/evs108 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595028 http://www.ncbi.nlm.nih.gov/pubmed/23196969 http://dx.doi.org/10.1093/gbe/evs108 © The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY-NC Research Article Text 2013 ftpubmed https://doi.org/10.1093/gbe/evs108 2013-09-04T21:00:16Z Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modifications, including high mitochondrial densities in aerobic tissues. A genomic expansion accompanying the evolution of these fish was reported, but paucity of genomic information limits the understanding of notothenioid cold adaptation. We reconstructed and annotated the first skeletal muscle transcriptome of the icefish Chionodraco hamatus providing a new resource for icefish genomics (http://compgen.bio.unipd.it/chamatusbase/, last accessed December 12, 2012). We exploited deep sequencing of this energy-dependent tissue to test the hypothesis of selective duplication of genes involved in mitochondrial function. We developed a bioinformatic approach to univocally assign C. hamatus transcripts to orthology groups extracted from phylogenetic trees of five model species. Chionodraco hamatus duplicates were recorded for each orthology group allowing the identification of duplicated genes specific to the icefish lineage. Significantly more duplicates were found in the icefish when transcriptome data were compared with whole-genome data of model species. Indeed, duplicated genes were significantly enriched in proteins with mitochondrial localization, involved in mitochondrial function and biogenesis. In cold conditions and without oxygen-carrying proteins, energy production is challenging. The combination of high mitochondrial densities and the maintenance of duplicated genes involved in mitochondrial biogenesis and aerobic respiration might confer a selective advantage by improving oxygen diffusion and energy supply to aerobic tissues. Our results provide new insights into the genomic basis of icefish cold adaptation. Text Antarc* Antarctic Icefish PubMed Central (PMC) Antarctic Genome Biology and Evolution 5 1 45 60 |
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Research Article Coppe, Alessandro Agostini, Cecilia Marino, Ilaria A.M. Zane, Lorenzo Bargelloni, Luca Bortoluzzi, Stefania Patarnello, Tomaso Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function |
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Research Article |
description |
Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modifications, including high mitochondrial densities in aerobic tissues. A genomic expansion accompanying the evolution of these fish was reported, but paucity of genomic information limits the understanding of notothenioid cold adaptation. We reconstructed and annotated the first skeletal muscle transcriptome of the icefish Chionodraco hamatus providing a new resource for icefish genomics (http://compgen.bio.unipd.it/chamatusbase/, last accessed December 12, 2012). We exploited deep sequencing of this energy-dependent tissue to test the hypothesis of selective duplication of genes involved in mitochondrial function. We developed a bioinformatic approach to univocally assign C. hamatus transcripts to orthology groups extracted from phylogenetic trees of five model species. Chionodraco hamatus duplicates were recorded for each orthology group allowing the identification of duplicated genes specific to the icefish lineage. Significantly more duplicates were found in the icefish when transcriptome data were compared with whole-genome data of model species. Indeed, duplicated genes were significantly enriched in proteins with mitochondrial localization, involved in mitochondrial function and biogenesis. In cold conditions and without oxygen-carrying proteins, energy production is challenging. The combination of high mitochondrial densities and the maintenance of duplicated genes involved in mitochondrial biogenesis and aerobic respiration might confer a selective advantage by improving oxygen diffusion and energy supply to aerobic tissues. Our results provide new insights into the genomic basis of icefish cold adaptation. |
format |
Text |
author |
Coppe, Alessandro Agostini, Cecilia Marino, Ilaria A.M. Zane, Lorenzo Bargelloni, Luca Bortoluzzi, Stefania Patarnello, Tomaso |
author_facet |
Coppe, Alessandro Agostini, Cecilia Marino, Ilaria A.M. Zane, Lorenzo Bargelloni, Luca Bortoluzzi, Stefania Patarnello, Tomaso |
author_sort |
Coppe, Alessandro |
title |
Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function |
title_short |
Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function |
title_full |
Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function |
title_fullStr |
Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function |
title_full_unstemmed |
Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function |
title_sort |
genome evolution in the cold: antarctic icefish muscle transcriptome reveals selective duplications increasing mitochondrial function |
publisher |
Oxford University Press |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595028 http://www.ncbi.nlm.nih.gov/pubmed/23196969 https://doi.org/10.1093/gbe/evs108 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Icefish |
genre_facet |
Antarc* Antarctic Icefish |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595028 http://www.ncbi.nlm.nih.gov/pubmed/23196969 http://dx.doi.org/10.1093/gbe/evs108 |
op_rights |
© The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1093/gbe/evs108 |
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Genome Biology and Evolution |
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5 |
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1 |
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45 |
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60 |
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1766277154481373184 |