Study On The Virome Of Peach And Its Wild Relative Species

Peach(Prunus persica L.)is a stone fruit tree species of high economic value.China is the world's largest country of peach production and consumption.However,peach trees are susceptible to various viral infections during their growth and development.Viral infections may affect the growth,development,and production of peach trees,and further,threat peach production and sustainable development of the peach industry.At present,there is a lack of comprehensive knowledge about species composition of peach viruses,their occurrence,genetic diversity,and genetic evolution in different peach germplasm trees in China.In this study,high-throughput sequencing was used to identify viruses in peach and its wild relative species(118 peach accessions),show the differences of virus composition from peach and its wild relative species,and analyze the genetic diversity and genetic evolution of these viruses.Firstly,the virus species and composition of 118 peach accession samples from 4 botanical species of peach and its wild relatives.Comparing RNA-seq(RNA sequencing)with sRNA sequencing,it is found that RNA-seq were much better than sRNA sequencing for obtaining the complete viral genome sequence and more species viruses.Therefore,RNA-seq was used for virus identification from 118 peach accession samples in the present study.After RT-PCR verification,a total of 15 known plant viruses,two species of viroids and five new viruses were identified.Among them,the most common viruses and viroids were peach-associated luteovirus,prunus necrotic ringspot virus,peach virus D,plum bark necrosis stem pitting-associated virus,nectarine stem pitting-associated virus,and peach latent mosaic virus.The virus species and composition of peach and its wild relative species were analyzed.It was found that there were 19,4,5 and 4 virus species in Prunus mira,Prunus davidiana,Prunus kansuensis,Prunus persica,respectively.Among them,14 virus species were only detected in Prunus persica,indicating that the virus species and composition of peach and its wild relative species were quite different.In addition,it was found that the number and composition of virus species in 4 kinds of common peach(ornamental peach,local variety group,cultivar,and rootstock)were similar.Secondly,the population diversity and genetic evolution of several major viruses were analyzed based on high-throughput sequencing data.Single nucleotide diversity(SNP)analysis showed that the SNP frequency of prunus virus 2 was the highest,that of prunus necrotic ringspot virus was the lowest,and that SNP sites were not obvious hot spots in each virus genome.Sequence alignment and genetic evolution analysis showed that these isolates of peach-associated luteovirus were clustered in three branches on the genetic evolution tree,these isolates of nectarine stem pitting-associated virus were clustered in two branches on the genetic evolution tree,but these isolates of peach leaf pitting-associated virus did not form obvious clustering on the genetic evolution tree.Finally,the genome sequence,genomic organization,taxonomic position and biological characteristics of five new viruses were verified and analyzed.RP19-1 and RP19-2 genomic sequences were amplified,which encode three overlapping open reading frames(ORFs).Sequence diversity and genetic evolution analysis showed that RP19-1,RP19-2,and Ta Tao 5 belong to the new virus species of genus Trichovirus: Peach chlorotic leaf spot virus.Peach virus 1,with a genome of 13,949 nt and encoding six ORFs.It is a new virus species from the genus Alphanucleorhabdovirus,which can be transmitted through grafting.This is the first report of negative-sense ssRNA virus detected in peach.Peach virus 2,with a genome of 4,978 nt and encoding two ORFs.It is a new virus species from the genus Totivirus.Its virus particles are icosahedral symmetrical structure(average diameter is about 30 nm).This is the first report of dsRNA virus detected in peach.Only two long segments of peach virus 3 and peach virus 4 were amplified,and their sequence diversity and genetic evolution analysis showed that they belonged to the genus Maculavirus.To conclude,a total of 15 known plant viruses,two viroids and five new viruses were identified from 118 peach accessions by high-throughput sequencing.The virus compositions of peach and its wild relative species,and the genetic diversity and genetic evolution of the main peach viruses were determined.These results are basic and important in our understanding the diversity and evolution of peach tree viruses and constructing more effective management measures to control viral diseases in peach production industry.