The Study Of Endogenous Double-stranded DNA Viruses In Eukaryotes

Double-stranded DNA viruses(dsDNA viruses)use double-stranded DNA as their genetic materials and replicate through DNA-dependent DNA polymerases.dsDNA viruses are highly diverse,including nucleocytoplasmic large DNA viruses,herpesviruses,baculoviruses,nudiviruses,polydnaviruses,and so on.Occasionally,dsDNA viruses can infect germ cells and become integrated into host genomes,forming endogenous dsDNA viral elements.Endogenous viral elements offer important “molecular fossils” for studying the diversity of ancient viruses as well as the co-evolutionary history between viruses and hosts.To date,endogenous dsDNA viruses have not been systematically mined and studied within the eukaryote genomes.Here,we use a comparative genomics method to systematically mine endogenous dsDNA viral elements in the eukaryote genomes.Our study finds that endogenous dsDNA viral elements are widely present in the genomes of fungi,animals(fishes,insects,and mammals),protists,and plants.We also perform phylogenetic analyses of sequences from dsDNA viruses,eukaryotes,archaea,and phages to explore the evolutionary position of the newly discovered endogenous dsDNA viruses within dsDNA viruses.Our study identifies numerous dsDNA viral elements,expands the diversity of dsDNA viruses,and provides novel insights into the classification,origins,evolution,and transmission modes of dsDNA viruses.We also performed detailed analyses of endogenous dsDNA viral elements identified within the genomes of fungi and insects.Currently,little is known about dsDNA virus infections in fungi.This study uses a comparative genomics and phylogenetic analysis combined approach to screen endogenous dsDNA viral elements within the fungal genomes.This study identifies two groups of endogenous nucleocytoplasmic large DNA viruses(NCLDVs),designated as fungus dsDNA alpha virus(fundsalphavirus)and fungus dsDNA beta virus(fundsbetavirus).While fundsalphavirus infects at least six fungal phyla and is closely related to the giant virus Pithovirus,fundsbetavirus can infect species among Glomeromycota and is closely related to African swine fever virus.Co-speciation analyses show that the evolution of fundsalphavirus evolved through frequent cross-species transmission.Our findings reveal that the host ranges of fundsalphavirus and fundsbetavirus cover nearly a third of known fungal phyla,suggesting dsDNA viruses widely infect fungi.Polydnaviruses are obligate mutualists of parasitoid wasps and include two genera,Bracovirus and Ichnovirus.Bracoviruses are thought to be derived from an ancestral nudivirus integrated into the ancestor of microgastroid complex approximately 100 million years ago.However,the known nudiviruses are only distantly related to bracoviruses.This study employs a paleovirological method to search for endogenous nudivirus-like elements within the arthropod genomes.Interestingly,numerous endogenous nudivirus-like elements are identified across the genome of Eurytoma brunniventris.Among these endogenous nudivirus-like elements,we find 14 core gene sequences might be derived from a betanudivirus,termed as Ebr ENV-?.Phylogenomic analyses show that Ebr ENV-? is the sister group to bracoviruses,indicating that Ebr ENV-? is the known closest relative of bracoviruses.Synteny analysis shows the order of core genes is not well conserved between Ebr ENV-? and nudiviruses,suggesting the highly dynamic nature of nudivirus genome evolution.The discovery of Ebr ENV-? bridges the evolutionary gap between bracoviruses and nudiviruses,and provides novel clues for the origin and evolution of polydnaviruses.Our study reveals the extraordinary diversity endogenous dsDNA viruses within the eukaryote genomes,which has important implications in our understanding of the diversity,evolution,and host range of dsDNA viruses.