泡沫病毒(FV)是研究病毒与其宿主之间长期进化史的理想模型。目前,在几乎所有脊椎动物的主要类群中都有FV的记录,但是软骨鱼中缺乏真正的FV浸润的证据,最基本的活脊椎动物,有颌骨。这里,我们筛选了软骨鱼的11个可用基因组和10个转录组序列集合,并揭示了一种新型的内源性泡沫病毒,软骨鱼内源性泡沫病毒(CFEFV),在鲨鱼和射线的基因组中。CFEFV的基因组分析揭示了在规范FV中保留的特征基序。使用聚合酶序列的系统发育分析揭示了CFEFV对脊椎动物FV的生根性质,表明他们的起源很深。有趣的是,在鲨鱼(Scyliorhinustorazame)中发现了三个病毒谱系,其中一种是鱼翅泡沫样病毒,表明该物种发生了多次病毒浸润。这些发现填补了Spumaretrovirinae分类单元的主要空白,并揭示了陆生脊椎动物中FV的水生起源。重要性尽管在脊椎动物的主要分支中发现了泡沫病毒(FV),这些病毒在软骨鱼中的存在,最基础的活脊椎动物,还有待探索。这项研究通过计算机基因组挖掘揭示了鲨鱼和射线中软骨内源性FV的集合。这些病毒根植于聚合酶(POL)系统发育,表明FV的古老水生起源。然而,它们的包膜(ENV)蛋白与两栖动物FV的包膜蛋白组合在一起,提示不同FV基因的不同进化史。总的来说,我们为Spumaretrovirinae的分类学研究提供了最后一个缺失的空白,并为FV的水生起源提供了具体支持。
Foamy viruses (FVs) are ideal models for studying the long-term evolutionary history between viruses and their hosts. Currently, FVs have been documented in nearly all major taxa of vertebrates, but evidence is lacking for true FV infiltration in cartilaginous fish, the most basal living vertebrates with jaws. Here, we screened 11 available genomes and 10 transcriptome sequence assemblies of cartilaginous fish and revealed a novel endogenous foamy virus, termed cartilaginous fish endogenous foamy virus (CFEFV), in the genomes of sharks and rays. Genomic analysis of CFEFVs revealed feature motifs that were retained among canonical FVs. Phylogenetic analysis using polymerase sequences revealed the rooting nature of CFEFVs to vertebrate FVs, indicating their deep origin. Interestingly, three viral lineages were found in a shark (Scyliorhinus torazame), one of which was clustered with ray-finned fish foamy-like viruses, indicating that multiple episodes of viral infiltrations had occurred in this species. These findings fill a major gap in the Spumaretrovirinae taxon and reveal the aquatic origin of FVs found in terrestrial vertebrates. IMPORTANCE Although foamy viruses (FVs) have been found in major branches of vertebrates, the presence of these viruses in cartilaginous fish, the most basal living vertebrates with jaws, remains to be explored. This study revealed a collection of cartilaginous endogenous FVs in sharks and rays through in silico genomic mining. These viruses were rooted in the polymerase (POL) phylogeny, indicating the ancient aquatic origin of FVs. However, their envelope (ENV) protein grouped with those of amphibian FVs, suggesting different evolutionary histories of different FV genes. Overall, we provide the last missing gap for the taxonomic investigation of Spumaretrovirinae and provide concrete support for the aquatic origin of FVs.