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）近年来作为介导基因表达转录后调控的新型因子而备受瞩目。miRNA基因在其所在的演化支中呈现高度保守性，因此被用作一类罕见的基因组变异性状，通过追踪其获得与缺失事件来推断系统发育关系。然而，其仅21~23碱基对（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。本研究借助系统发育关系已明确的参考分类群，证实miRNA序列在系统发育分析中可发挥出色的定量分析效用，而非仅局限于定性分析。不同物种的miRNA基因间明确的直系同源关系，使得即便仅使用碎片化的数据集，也可便捷地完成序列的鉴定与比对。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，并证实该保守区域同样可用于系统发育分析，同时也为其他研究领域明确了值得关注的保守序列区段。本研究利用12个已测序果蝇科物种基因组中的miRNA序列，并以赤拟谷盗（Tribolium castaneum）作为外类群，通过贝叶斯法与最大似然法验证了该方法的稳健性。该类性状的应用潜力在杆形线虫目线虫与灵长类类群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全新的备选数据源。该方法可快速解析亲缘关系较近以及快速演化物种间的系统发育关系，同时为探究生命之树内的各类演化关系提供了又一有力工具。