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，基因组的绝大部分区域均可发生转录，但此类转录的生物学意义迄今仍存在广泛争议。本研究针对小鼠属（Mus）的多个类群开展全面采样，覆盖长达10 Myr的系统发育距离，以此表征多聚腺苷酸化转录本（poly-adenylated transcripts）的系统发育周转（phylogenetic turnover）特征。借助深度RNA测序技术，我们发现：在单一类群内部，转录组覆盖度（transcriptome coverage）会随测序深度增加达到饱和；但跨类群比较时，即便处于这一较浅的系统发育尺度下，转录组覆盖范围仍会持续拓展。我们的数据显示，不同类群间的转录状态（transcriptional states）存在高度更替，且在进化时间尺度上不存在显著的转录游离岛（transcript-free islands）。这一结果提示，从进化时间维度审视时，整个基因组均可被转录为多聚腺苷酸化RNA。综上，我们认为非编码基因组（non-coding genome）的任意区域，均有可能在相对较短的进化时间尺度内，通过从头基因进化（de novo gene evolution）获得演化功能性。