Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, UK.
Animal Genomics, ETH Zurich, Zurich, Switzerland.
BMC Evol Biol. 2019 May 8;19(1):99. doi: 10.1186/s12862-019-1425-0.
RNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit high levels of adaptive substitution, and over longer timescales show gene duplication and loss-most likely as a consequence of their role in mediating conflict with these parasites. This is particularly striking for Argonaute 2 (Ago2), which is ancestrally the key effector of antiviral RNAi in insects, but has repeatedly formed new testis-specific duplicates in the recent history of the obscura species-group of Drosophila.
Here we take advantage of publicly available genomic and transcriptomic data to identify six further RNAi-pathway genes that have duplicated in this clade of Drosophila, and examine their evolutionary history. As seen for Ago2, we observe high levels of adaptive amino-acid substitution and changes in sex-biased expression in many of the paralogs. However, our phylogenetic analysis suggests that co-duplications of the RNAi machinery were not synchronous, and our expression analysis fails to identify consistent male-specific expression.
These results confirm that RNAi genes, including genes of the antiviral and piRNA pathways, have undergone multiple independent duplications and that their history has been particularly labile within the obscura group. However, they also suggest that the selective pressures driving these changes have not been consistent, implying that more than one selective agent may be responsible.
RNA 干扰（RNAi）相关途径为抗病毒和转座元件提供防御，并且与减数分裂驱动元件的抑制有关。这些途径中的基因通常表现出高水平的适应性替代，并且在更长的时间尺度上显示基因复制和丢失-很可能是由于它们在介导与这些寄生虫的冲突方面的作用。这在 Argonaute 2（Ago2）中尤为明显，Ago2 是昆虫抗病毒 RNAi 的主要效应因子，但在果蝇 obscura 种组的近代历史中，它已反复形成新的睾丸特异性重复基因。
在这里，我们利用公开的基因组和转录组数据，鉴定了在这个果蝇分支中重复的另外六个 RNAi 途径基因，并研究了它们的进化历史。与 Ago2 一样，我们观察到许多旁系同源物中存在高水平的适应性氨基酸替代和性别偏向表达的变化。然而，我们的系统发育分析表明，RNAi 机制的共复制不是同步的，我们的表达分析也未能确定一致的雄性特异性表达。
这些结果证实，RNAi 基因，包括抗病毒和 piRNA 途径的基因，已经经历了多次独立的复制，并且在 obscura 组内它们的历史特别不稳定。然而，它们也表明，推动这些变化的选择压力并不一致，这意味着不止一个选择因子可能是负责的。
