To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.

评估整个果蝇中的miRNA进化属下，我们分析了12种果蝇物种中数十亿个小RNA的读数。这些数据可以全面鉴定miRNA身份，丰度和加工过程中特定物种和进化枝的变异。在保存良好的miRNA中，我们观察到5'末端精确度进化枝特异性变异的意外情况，偶然的反义基因座和推定的非经典基因座。我们还使用严格的标准来鉴定一大套（649）新颖的，受进化限制的miRNA。在大量的受物种限制的miRNA集合中，两个显着的亚群是剪接衍生的mirtrons和睾丸受限制的，最近进化的，成簇的（TRC）规范miRNA。我们使用注解和系统发育模型量化了miRNA的出生和死亡，以估算miRNA转换率。果蝇进化枝。特别是，不同的miRNA类型的不同进化行为是不同分子原理的基础。Mirtrons与3'非模板化添加的高比率相关，这是阻止其生物发生的机制，而TRC miRNA似乎在正选择下进化。总而言之，这些数据揭示了果蝇物种之间的miRNA多样性以及其出现和进化的基础原理。