Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence
Abstract
Deep sequencing analyses have shown that a large fraction of genomes is transcribed, but the significance of this transcription is much debated. Here, we characterize the phylogenetic turnover of poly-adenylated transcripts in a comprehensive sampling of taxa of the mouse (genus Mus), spanning a phylogenetic distance of 10 Myr. Using deep RNA sequencing we find that at a given sequencing depth transcriptome coverage becomes saturated within a taxon, but keeps extending when compared between taxa, even at this very shallow phylogenetic level. Our data show a high turnover of transcriptional states between taxa and that no major transcript-free islands exist across evolutionary time. This suggests that the entire genome can be transcribed into poly-adenylated RNA when viewed at an evolutionary time scale. We conclude that any part of the non-coding genome can potentially become subject to evolutionary functionalization via de novo gene evolution within relatively short evolutionary time spans.
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Ethics
Animal experimentation: All mice were obtained from the mouse collection at the Max Planck Institute for Evolutionary Biology, following standard rearing techniques which ensure a homogeneous environment for all animals. Mice were maintained and handled in accordance to FELASA guidelines and German animal welfare law (Tierschutzgesetz {section sign} 11, permit from Veterinäramt Kreis Plön: 1401-144/PLÖ-004697).
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© 2016, Neme & Tautz
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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