NGS Mining RNA Viruses Diversity And Phylogenetic Analysis In The Plant-parasitic Nematodes

Plant-parasitic nematodes are one of the important pathogens of crop,which cause substantial crop yield reduction and serious economic losses every year,but research on plant-parasitic nematode viruses is scarce.Revealing the virus species in plant-parasitic nematodes will provide resources for the study of virus evolution and plant-parasitic nematode bio-control viruses.In this study,the meta-transcriptome library of root-knot nematodes and Ditylenchus destructor was constructed by sampling nematode disease samples,parasitic nematode isolation and nucleic acid extraction.We also combined with transcriptome of plant-parasitic nematode in public databases to analyzed diversity and genomic characteristics of viruses in plant-parasitic nematodes.The detailed results of the study are as follows:The sequence information of 50 different RNA viruses was obtained,and the complete genome sequences or complete single-segment genome sequences of 7nematode viruses were obtained.Based on database alignment analysis,14 different viral sequences were identified in the meta-transcriptome library of Ditylenchus destructor,including 13 potentially novel viruses and 1 nodavirus(SANTV)that has been reported in Caenorhabditis briggsae.A total of 36 viral sequences containing complete Rd Rp regions were identified in the transcriptome of the nematode,of which 25 were less similar to known viral genome sequences and were considered potentially novel RNA viruses.Another 11 viruses have been reported in plant-parasitic nematodes.We identified 50 viruses,of which 50% were single-stranded negative-sence RNA viruses across 7 families,including members of the Phenuiviridae,Discoviridae,Rhabdoviridae,Nyamiviridae,Yueviridae,Qinviridae and Orthomyxoviridae.The 24 plant-parasitic nematode viruses were single-stranded positive-sence RNA viruses form the families Nodaviridae,Endornaviridae,Bromoviridae,Flaviviridae,Marnaviridae and Dicistroviridae.The remaining one was double-stranded RNA virus from Birnaviridae,and this is the first time that double-stranded RNA viruses have been discovered in plant-parasitic nematodes.DNA viruses information was not found in transcriptome of plant-parasitic nematode.In total,the study identified 50 RNA viruses hosting plant-parasitic nematodes,revealing the diversity of nematode viruses.In the phylogenetic analysis based on Rd Rp protein,nematode viruses in the same virus taxa tend to cluster in the same branch,showing obvious host specificity.At the same time,the investigation of virus host range and distribution showed that most plant-parasitic nematode viruses can infect multiple nematode species,reflecting the species diversity and widespread distribution of nematode virus hosts.The analysis is of great significance for the improvement of the evolutionary history of viruses,and provides support for the rational utilization of nematode virus resources.