Discovery of novel non-retroviral endogenous viral elements reveals their long-term integration history in spiders

Endogenous viral elements (EVEs) are widespread in the genomes of various organisms and have played a crucial role in evolution. Historically, research on EVEs primarily focused on those derived from retroviruses; however, the significance of non-retroviral EVEs (nrEVEs) has gradually gained recognition. In this study, we employ an approach that combines protein structure prediction with sequence analysis to identify a large group of previously unrecognized nrEVEs across spider genomes. Additionally, we identify nrEVE-related messenger RNAs, small interfering RNAs, and PIWI-interacting RNAs in spiders, suggesting that these nrEVEs may be functionally active. We also experimentally confirm the presence of spider nrEVEs and their transcripts in individual spiders. Evolutionary analysis suggests that these spider nrEVEs derived from unidentified nuclear arthropod large DNA viruses belonging to the order Lefavirales, class Naldaviricetes. Multiple integration events must have occurred both anciently and recently during the evolutionary history of spiders to explain these nrEVEs. Our findings reveal a novel group of nrEVEs and provide valuable insights into their evolutionary relationship with arthropods.

内源性病毒元件（endogenous viral elements, EVEs）广泛存在于各类生物的基因组中，在生物演化进程中发挥了关键作用。历史上，针对EVEs的研究主要聚焦于逆转录病毒来源的该类元件；然而非逆转录病毒来源的内源性病毒元件（non-retroviral EVEs, nrEVEs）的重要性正逐渐获得学界认可。本研究采用蛋白质结构预测与序列分析相结合的研究方法，在蜘蛛基因组中鉴定出了一大批此前未被发现的nrEVEs。此外，本研究在蜘蛛体内鉴定到了与nrEVEs相关的信使RNA（messenger RNA, mRNA）、小干扰RNA（small interfering RNA, siRNA）以及PIWI互作RNA（PIWI-interacting RNA, piRNA），这表明此类nrEVEs可能具备功能活性。本研究还通过实验验证了单个蜘蛛体内蜘蛛nrEVEs及其转录本的存在。演化分析结果显示，这些蜘蛛nrEVEs源自隶属于Naldaviricetes纲、Lefavirales目且尚未被鉴定的节肢动物核大型DNA病毒。要解释此类nrEVEs的存在，必然需要假定在蜘蛛的演化历史中，既发生过远古时期的多次整合事件，也存在近期的整合事件。本研究的发现揭示了一类全新的nrEVEs，并为解析其与节肢动物的演化关联提供了重要参考。