title: 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.
authors.affiliation: Max-Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Rafik
authors.identifier: http://orcid.org/0000-0001-8462-5291
authors.initials: R
authors.lastname: Neme
authors.affiliation: Max-Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Diethard
authors.identifier: http://orcid.org/0000-0002-0460-5344
authors.initials: D
authors.lastname: Tautz
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice / Q000235:genetics*; D014158:Transcription, Genetic
keywords: de novo genes; evolution; evolutionary biology; genomics; mouse; transcriptome
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