Data from: Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

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.

深度测序（deep sequencing）分析已证实，基因组的绝大多数区域均可发生转录，但此类转录的生物学意义仍存在广泛争议。在此研究中，我们针对小鼠属（Mus）的类群（taxa）开展全面采样，覆盖了10百万年（Myr）的进化距离，以此解析聚腺苷酸化转录本（poly-adenylated transcripts）的谱系更替（phylogenetic turnover）特征。借助深度RNA测序（deep RNA sequencing）技术，我们发现：在单个类群内，转录组覆盖度会在特定测序深度下达到饱和；但在不同类群间进行比较时，即便处于如此浅的系统发育尺度下，转录组覆盖度仍会持续扩展。本研究数据显示，不同类群间的转录状态存在高度更替，且在整个进化历程中，不存在大规模的无转录岛（transcript-free islands）。这一结果表明，若从进化时间尺度来看，整个基因组均可被转录为聚腺苷酸化RNA（poly-adenylated RNA）。综上我们得出结论：在相对较短的进化时间跨度内，非编码基因组（non-coding genome）的任意区域，均有可能通过从头基因进化（de novo gene evolution）经历进化功能化（evolutionary functionalization）。