Analysis Of Endogenous Petunia Vein Clearing Virus Like Sequences In The Rice Genome

Sequences of various DNA plant viruses integration into host plant genomes havebeen reported.Pararetroviruses integrated into the host genome are referred to as endogenous pararetroviruses(EPRV).Wheres our current understanding isinsufficient to fully describe the role of EPRV affects the function and evolutionof plant gene.We have addressed two questions as to endogenous RTBV;the insertion mechanism of ERTBV into rice genome and the relationship between ERTBV and RTBV resistance.The interplay of different virus species in a host cell after infection can affect the adaptation of each virus.Endogenous viral elements,such as endogenous pararetroviruses(PRVs),have arisen from vertical inheritance of viral sequences integrated into host germline genomes.As viral genomic fossils,these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions but have rarely been applied for this purpose.All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells.Here,we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through virus-virus interactions.Paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have interacted with autonomous PRVs in a parasitic partnership or with one another in a mutualistic partnership.These partnerships,which have been established by the sharing of noncoding regulatory sequences(NRSs)in intergenic regions between two partner viruses,have been further maintained and altered by the convergence of NRSs between partners.Strikingly,we found that frequent region-specific recombination rather than mutation selection,is the main causative mechanism of NRS convergence.Our results,obtained from ancient DNA records of viruses,suggest that adaptation of PRVs has occurred by exchange of NRSs between different virus species in the same host;they further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.