Lewis Samuel H, Salmela Heli, Obbard Darren J
Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present Address: Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH
Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, Finland.
Genome Biol Evol. 2016 Feb 11;8(3):507-18. doi: 10.1093/gbe/evw018.
Genetic studies of Drosophila melanogaster have provided a paradigm for RNA interference (RNAi) in arthropods, in which the microRNA and antiviral pathways are each mediated by a single Argonaute (Ago1 and Ago2) and germline suppression of transposable elements is mediated by a trio of Piwi-subfamily Argonaute proteins (Ago3, Aub, and Piwi). Without a suitable evolutionary context, deviations from this can be interpreted as derived or idiosyncratic. Here we analyze the evolution of Argonaute genes across the genomes and transcriptomes of 86 Dipteran species, showing that variation in copy number can occur rapidly, and that there is constant flux in some RNAi mechanisms. The lability of the RNAi pathways is illustrated by the divergence of Aub and Piwi (182-156 Ma), independent origins of multiple Piwi-family genes in Aedes mosquitoes (less than 25Ma), and the recent duplications of Ago2 and Ago3 in the tsetse fly Glossina morsitans. In each case the tissue specificity of these genes has altered, suggesting functional divergence or innovation, and consistent with the action of dynamic selection pressures across the Argonaute gene family. We find there are large differences in evolutionary rates and gene turnover between pathways, and that paralogs of Ago2, Ago3, and Piwi/Aub show contrasting rates of evolution after duplication. This suggests that Argonautes undergo frequent evolutionary expansions that facilitate functional divergence.
黑腹果蝇的遗传学研究为节肢动物中的RNA干扰（RNAi）提供了一个范例，其中微小RNA和抗病毒途径分别由单个AGO蛋白（AGO1和AGO2）介导，而转座元件的种系抑制则由一组Piwi亚家族AGO蛋白（AGO3、Aub和Piwi）介导。如果没有合适的进化背景，与之不同的情况可能会被解释为衍生的或特异的。在这里，我们分析了86种双翅目物种的基因组和转录组中AGO基因的进化情况，结果表明拷贝数的变化可能会迅速发生，并且一些RNAi机制处于持续的动态变化中。RNAi途径的不稳定性体现在Aub和Piwi的分化（1.82 - 1.56亿年前）、伊蚊中多个Piwi家族基因的独立起源（不到2500万年前）以及采采蝇舌蝇中AGO2和AGO3的近期重复。在每种情况下，这些基因的组织特异性都发生了改变，这表明功能发生了分化或创新，并且与AGO基因家族中动态选择压力的作用相一致。我们发现不同途径之间的进化速率和基因更替存在很大差异，并且AGO2、AGO3和Piwi/Aub的旁系同源基因在复制后显示出不同的进化速率。这表明AGO蛋白经历频繁的进化扩张，从而促进功能分化。
