State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China.
J Virol. 2024 Oct 22;98(10):e0099724. doi: 10.1128/jvi.00997-24. Epub 2024 Aug 30.
Negevirus is a recently proposed taxon of arthropod-infecting virus, which is associated with plant viruses of two families ( and ). Nevertheless, the evolutionary history of negevirus-host and its relationship with plant viruses remain poorly understood. Endogenous nege-like viral elements (ENVEs) are ancient nege-like viral sequences integrated into the arthropod genomes, which can serve as the molecular fossil records of previous viral infection. In this study, 292 ENVEs were identified in 150 published arthropod genomes, revealing the evolutionary history of nege-like viruses and two related plant virus families. We discovered three novel and eight strains of nege-like viruses in 11 aphid species. Further analysis indicated that 10 ENVEs were detected in six aphid genomes, and they were divided into four types (ENVE1-ENVE4). Orthologous integration and phylogenetic analyses revealed that nege-like viruses had a history of infection of over 60 My and coexisted with aphid ancestors throughout the Cenozoic Era. Moreover, two nege-like viral proteins (CP and SP24) were highly homologous to those of plant viruses in the families and . CP- and SP24-derived ENVEs were widely integrated into numerous arthropod genomes. These results demonstrate that nege-like viruses have a long-term coexistence with arthropod hosts and plant viruses of the two families, and , which may have evolved from the nege-like virus ancestor through horizontal virus transfer events. These findings broaden our perspective on the history of viral infection in arthropods and the origins of plant viruses.
Although negevirus is phylogenetically related to plant virus, the evolutionary history of negevirus-host and its relationship with plant virus remain largely unknown. In this study, we used endogenous nege-like viral elements (ENVEs) as the molecular fossil records to investigate the history of nege-like viral infection in arthropod hosts and the evolution of two related plant virus families ( and ). Our results showed the infection of nege-like viruses for over 60 My during the arthropod evolution. ENVEs highly homologous to viral sequences in and were present in a wide range of arthropod genomes but were absent in plant genomes, indicating that plant viruses in these two families possibly evolved from the nege-like virus ancestor through cross-species horizontal virus transmission. Our findings provide a new perspective on the virus-host coevolution and the origins of plant viruses.
节古病毒是一种最近提出的节肢动物感染病毒分类群，与两个科的植物病毒有关（ 和 ）。然而，节古病毒-宿主的进化历史及其与植物病毒的关系仍知之甚少。内源性节古样病毒元件（ENVEs）是整合到节肢动物基因组中的古老节古样病毒序列，可作为先前病毒感染的分子化石记录。在这项研究中，在 150 个已发表的节肢动物基因组中鉴定出 292 个 ENVEs，揭示了节古样病毒和两个相关植物病毒科的进化历史。我们在 11 种蚜虫中发现了三种新型和八种节古样病毒。进一步的分析表明，在 6 个蚜虫基因组中检测到 10 个 ENVEs，它们分为四种类型（ENVE1-ENVE4）。直系同源整合和系统发育分析表明，节古样病毒的感染历史超过 6000 万年，并与新生代的蚜虫祖先共存。此外，两种节古样病毒蛋白（CP 和 SP24）与 和 科的植物病毒高度同源。CP 和 SP24 衍生的 ENVEs广泛整合到许多节肢动物基因组中。这些结果表明，节古样病毒与节肢动物宿主和 和 两个科的植物病毒长期共存，可能通过水平病毒转移事件从节古样病毒祖先进化而来。这些发现拓宽了我们对节肢动物病毒感染史和植物病毒起源的认识。
尽管节古病毒在系统发育上与植物病毒有关，但节古病毒-宿主的进化历史及其与植物病毒的关系在很大程度上仍不清楚。在这项研究中，我们使用内源性节古样病毒元件（ENVEs）作为分子化石记录，研究了节古样病毒在节肢动物宿主中的感染历史以及两个相关植物病毒科（ 和 ）的进化。我们的结果表明，在节肢动物进化过程中，节古样病毒感染超过 6000 万年。在广泛的节肢动物基因组中存在与 和 科病毒序列高度同源的 ENVEs，但在植物基因组中不存在，这表明这两个科的植物病毒可能通过跨物种水平病毒传播从节古样病毒祖先进化而来。我们的研究结果为病毒-宿主共同进化和植物病毒的起源提供了新的视角。
