Rampant Nuclear Insertion of mtDNA across Diverse Lineages within Orthoptera (Insecta)

Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.核线粒体假基因（nuclear mitochondrial pseudogenes，numts）是插入核基因组中的线粒体DNA（mitochondrial DNA，mtDNA）非功能片段。该类假基因广泛分布于真核生物类群，且其数量与基因组大小呈显著正相关。既往多数核线粒体假基因相关研究均以核基因组已完成全测序的模式生物为研究对象，但此类分析难以针对任意特定类群，就核线粒体假基因的积累模式作出普遍性推断。 在昆虫纲中，直翅目（Orthoptera）不仅拥有目前已知最大的核基因组，同时该类群中也包含多个核线粒体假基因数量庞大的物种。本研究以直翅目为案例类群，针对覆盖该目系统发育多样性的28个直翅目科中的3个线粒体基因座开展核线粒体假基因预测，以解析该类群中核线粒体假基因的多样性与丰度。研究发现，核线粒体假基因在所有演化支中均广泛存在，但不同演化支间并未呈现出可识别且一致的假基因积累模式。同样，本研究未发现任何证据表明某类线粒体基因相较其他基因更易发生核插入事件。此外，研究证实核线粒体假基因的插入事件在直翅目物种分化历程中持续且频繁地发生。尽管多数核线粒体假基因均为近期核插入事件的产物，但本研究仍发现了可追溯至侏罗纪时期的古老核线粒体假基因插入证据，这类古老假基因在亲缘关系高度分歧的类群中均有留存。最后，本研究探讨了直翅目中核线粒体假基因极端富集的多项影响因素，并强调了探究核线粒体假基因在演化生物学研究中应用价值的重要性。