Studies On The Diversity And Evolution Of Vertebrate Endogenous Retroviruses

Retroviridae,a viral family of single-stranded RNA virus,can only infect vertebrates and cause many diseases in human and animals.The replication of retroviruses requires reverse-transcription of single-stranded RNA into DNA and integration into the host genome.Retroviruses usually infect somatic cells but can occasionally infect germ cells.When retroviruses infect host germ cells,the integrated retro-viruses,namely endogenous retroviruses(ERVs),begin to be inherited vertically from parent to offspring as part of the host genome.ERVs documented past retroviral infections and thus provide valuable"molecular fossils" for studying the deep history and long-term evolution of retroviruses.Previous studies have focused on ERVs in mammalian and avian genomes,and little is known about ERVs in other vertebrate genomes.In this study,we use a combined homology search and phylogenetic analysis approach to systematically mine ERVs in the genomes of 92 basal vertebrates(72 fishes,4 amphibians,and 16 reptiles).A total of 8,075 ERV sequences are identified,and 452 whole or partial genome sequences of ERVs are reconstructed.Phyloge netic analysis of newly identified ERVs and other representative retroviruses shows that retroviruses can be classified into five major lineages,providing novel insights into the classification and host distribution of retroviruses.To study the role of host-switching and co-divergence in the evolution of retroviruses,we perform host-virus co-phylogenetic tests and find that most of retroviral lineages(except foamy virus)underwent frequent cross-species transmission in basal vertebrates.We also find multiple independent events of retroviral transmission between terrestrial and aquatic vertebrates,indicating that the land-water barrier is not strong for the retrovirus transmission.In this study,we systematically dig and analyze ERVs in the genomes of basal vertebrates,which might help us to understand the diversity,classification,and evolution of retroviruses.