A Study Of The Diversity And Evolution Of Eukaryotic Retroviroids

Reverse-transcribing viruses are a group of viruses whose replication requires reverse transcription.Reverse-transcribing viruses infect a wide range of eukaryotes,and can cause various diseases in plants and animals.The International Committee on Taxonomy of Viruses(ICTV)unified reverse-transcibing viruses into a single viral order,Ortervirales.Currently,the order Ortervirale has been further divided into five families,namely Retroviridae,Caulimoviridae,Metaviridae(Ty3/Gypsy retrotransposons),Pseudoviridae(Ty1/Copia retrotransposons),and Belpaoviridae(Bel/Pao retrotransposons).The latter three are often referred to as Long terminal repeat(LTR)retrotransposons.Reverse-transcribing viruses have been thought to be ubiquitous in the eukaryote genomes and are a major component of eukaryote genomes.The extent of LTR retrotransposons has been frequently explored within a single or a limited number of species.LTR retrotransposons have been thought to be ubiquitous in the eukaryote genomes and contribute substantially to the evolution of eukaryote genome complexity.However,a comprehensive picture on the diversity and evolution of LTR retrotransposons across eukaryotes is still lacking.Here,we perform large-scale phylogenomics analyses of LTR retrotransposons within the genomes of 314 representative eukaryotes that cover the major diversity of eukaryotes.This study finds a very high diversity of LTR retrotransposons in eukaryote genomes,filling in the evolutionary gaps among known LTR retrotransposons.Paradoxically,although LTR retrotransposons exhibit unprecedented diversity,phylogenetic analyses show that they cluster into three major clades that correspond to Metaviridae(Ty3/Gypsy retrotransposons)/Retroviridae/Caulimoviridae,Pseudoviridae(Ty1/Copia retrotransposons),and Belpaoviridae(Bel-Pao retrotransposons),and no new major clade was identified.Metaviruses and pseudoviruses are widespread in eukaryote genomes,whereas belpaoviruses are only found in metazoa and some amoebae.Unexpectedly,this study did not identify LTR retrotransposons in the genomes of a large number of eukaryotes,indicating that many eukaryotes escaped the activity of LTR retrotransposons.The domain configurations of LTR retrotransposons appear to evolve in a modular fashion with frequent gains and losses of diverse new domains.Moreover,this study finds that massive horizontal transfer events occurred among distantly related eukaryote lineages in relatively recent time.Taken together,this study provides a unique and comprehensive framework to understand the evolution and diversity of LTR retrotransposons.