Journal Article

Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function

Alessandro Coppe, Cecilia Agostini, Ilaria A.M. Marino, Lorenzo Zane, Luca Bargelloni, Stefania Bortoluzzi and Tomaso Patarnello

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 5, issue 1, pages 45-60
Published in print January 2013 |
Published online November 2012 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evs108

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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.

Keywords: deep sequencing; orthology/paralogy relationships; gene duplication; genome evolution; cold adaptation; Channichthyidae

Journal Article.  9398 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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