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关键因子，逐渐成为学界关注的焦点。miRNA基因被认为在其所在的演化支中高度保守。因此，miRNA曾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开展系统发育推演。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。
本研究以系统发育关系已明确的参考类群为研究对象，证实miRNA序列在定量而非定性系统发育分析中具备极高应用价值。不同物种间miRNA基因明确的直系同源性，使得即便从碎片化的数据集内也可轻松识别并比对此类序列。此外，我们在miRNA基因的直接侧翼区域发现了显著的序列保守性，并证实该区域同样可用于系统发育分析，同时还锁定了其他研究领域感兴趣的保守区域。
本研究采用12个已测序果蝇类群的基因组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。此类性状的应用价值还在小杆线虫目（rhabditid nematodes）线虫与灵长类中得到了进一步证实。
随着下一代测序技术使基因组与小RNA文库的测序成本大幅降低，本方法为系统发育分析提供了一种全新的数据源。该策略能够快速解析亲缘关系较近以及快速演化物种间的演化关系，同时也为生命之树内部的亲缘关系研究提供了额外的研究工具。