Data from: The phylogenetic utility and functional constraint of microRNA flanking sequences

MicroRNAs (miRNAs) have recently risen to prominence as novel factors responsible for post-transcriptional regulation of gene expression. miRNA genes have been posited as highly conserved in the clades in which they exist. Consequently, miRNAs have been used as rare genome change characters to estimate phylogeny by tracking their gain and loss. However, their short length (21–23 bp) has limited their perceived utility in sequenced-based phylogenetic inference. Here, using reference taxa with established phylogenetic relationships, we demonstrate that miRNA sequences are of high utility in quantitative, rather than in qualitative, phylogenetic analysis. The clear orthology among miRNA genes from different species makes it straightforward to identify and align these sequences from even fragmentary datasets. We also identify significant sequence conservation in the regions directly flanking miRNA genes, and show that this too is of utility in phylogenetic analysis, as well as highlighting conserved regions that will be of interest to other fields. Employing miRNA sequences from 12 sequenced drosophilid genomes, together with a Tribolium castaneum outgroup, we demonstrate that this approach is robust using Bayesian and maximum-likelihood methods. The utility of these characters is further demonstrated in the rhabditid nematodes and primates. As next-generation sequencing makes it more cost-effective to sequence genomes and small RNA libraries, this methodology provides an alternative data source for phylogenetic analysis. The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.

微小RNA（MicroRNAs, miRNAs）近年来已成为介导基因表达转录后调控的新型关键因子而广受关注。已有研究表明，miRNA基因在其所在的进化枝中具有高度保守性。因此，miRNA被作为一类罕见的基因组变化性状，通过追踪其获得与丢失事件来推断系统发育关系。然而，其仅21~23 bp的较短长度限制了其在基于序列的系统发育推断中的应用潜力。本研究利用系统发育关系已明确的参考类群，证明miRNA序列在系统发育分析中具有极高的应用价值，且这种价值体现在定量分析而非定性分析层面。不同物种的miRNA基因间存在明确的直系同源关系，这使得即便从碎片化的数据集里也能轻松识别并比对这些序列。本研究还在miRNA基因的直接侧翼区域中发现了显著的序列保守性，并证明该区域同样可用于系统发育分析，同时还凸显了其他研究领域可能感兴趣的保守区域。本研究利用12个已测序果蝇科物种基因组中的miRNA序列，外加赤拟谷盗（Tribolium castaneum）作为外群，通过贝叶斯法与最大似然法验证了该方法的稳健性。该类性状的应用价值还在小杆线虫目线虫与灵长类中得到了进一步验证。随着下一代测序技术使得基因组与小RNA文库的测序成本大幅降低，该方法为系统发育分析提供了一种替代性数据源。该方法能够快速解析近缘物种与快速演化物种间的系统发育关系，同时为生命之树内各类群亲缘关系的研究提供了又一有力工具。