Department of Biology, Colorado State University, Fort Collins, CO, USA.
Department of Life and Environmental Sciences, University of California, Merced, CA, USA.
Genome Biol Evol. 2021 Mar 1;13(3). doi: 10.1093/gbe/evaa254.
Compared with free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to partition the effects of mutation versus selection. For example, the ancestor of Auchenorrhynchan insects contained two obligate endosymbionts, Sulcia and a betaproteobacterium (BetaSymb; called Nasuia in leafhoppers) that exhibit divergent rates of sequence evolution and different propensities for loss and replacement in the ensuing ∼300 Ma. Here, we use the auchenorrhynchan leafhopper Macrosteles sp. nr. severini, which retains both of the ancestral endosymbionts, to test the hypothesis that differences in evolutionary rate are driven by differential mutagenesis. We used a high-fidelity technique known as duplex sequencing to measure and compare low-frequency variants in each endosymbiont. Our direct detection of de novode novo mutations reveals that the rapidly evolving endosymbiont (Nasuia) has a much higher frequency of single-nucleotide variants than the more stable endosymbiont (Sulcia) and a mutation spectrum that is potentially even more AT-biased than implied by the 83.1% AT content of its genome. We show that indels are common in both endosymbionts but differ substantially in length and distribution around repetitive regions. Our results suggest that differences in long-term rates of sequence evolution in Sulcia versus BetaSymb, and perhaps the contrasting degrees of stability of their relationships with the host, are driven by differences in mutagenesis.
与自由生活的细菌相比，吸食植物汁液的昆虫内共生体具有微小且快速进化的基因组。遗传漂变增加、高突变率以及与宿主对关键细胞功能的控制相关的选择放松，都可能导致基因组退化。系统发育比较揭示了内共生体进化率的巨大差异，但这些方法很难将突变与选择的影响分开。例如，Auchenorrhynchan 昆虫的祖先包含两种必需的内共生体，Sulcia 和一种β变形菌（BetaSymb；在叶蝉中称为 Nasuia），它们表现出不同的序列进化速率和在随后的 3000 万年中不同的缺失和替代倾向。在这里，我们使用 Auchenorrhynchan 叶蝉 Macrosteles sp. nr. severini，它保留了两个祖先内共生体，来检验进化率差异是由不同的诱变驱动的假设。我们使用一种称为双链测序的高保真技术来测量和比较每个内共生体中的低频变体。我们对新出现的突变的直接检测表明，进化迅速的内共生体（Nasuia）的单核苷酸变体频率比更稳定的内共生体（Sulcia）高得多，而且其突变谱可能比其基因组 83.1%的 AT 含量所暗示的更偏向 AT。我们表明，插入缺失在两个内共生体中都很常见，但在重复区域周围的长度和分布上有很大差异。我们的结果表明，Sulcia 与 BetaSymb 之间长期序列进化率的差异，以及它们与宿主关系的稳定性的差异，是由诱变的差异驱动的。
