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New genes and functional innovation in mammals

José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M.Isabel Agea, Maria Gallo, David Andreu, M.Mar Albà
doi: https://doi.org/10.1101/090860
José Luis Villanueva-Cañas
1Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
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Jorge Ruiz-Orera
1Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
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M.Isabel Agea
1Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
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Maria Gallo
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
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David Andreu
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
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M.Mar Albà
1Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
3Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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  • For correspondence: malba@imim.es
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ABSTRACT

The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mamalian species, obtaining about 6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from non-coding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 29, 2017.
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New genes and functional innovation in mammals
José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M.Isabel Agea, Maria Gallo, David Andreu, M.Mar Albà
bioRxiv 090860; doi: https://doi.org/10.1101/090860
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New genes and functional innovation in mammals
José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M.Isabel Agea, Maria Gallo, David Andreu, M.Mar Albà
bioRxiv 090860; doi: https://doi.org/10.1101/090860

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