Genomics Diversity And Phylogenetic Analysis Of Plasmopara Viticola Of Chinese Wild And Euroasia Vitis Species

Grape downy mildew(DM)is one of the most important diseases affecting the yield and quality of grapes.Recently,with the extensive planting of different DM-resistant varieties and the quickly development of fungicide resistance,genetic diversity of Plasmopara viticola was obviously observed.Our previously research showed that the pathogenicity of the strains from different Vitis species was significantly different.In this study,population genomics of strains isolated from V.vinifera‘Red globe’,V.davidii and V.amurensis was analyzed based on the phylogeny of whole-genome to clarify the genetic differentiation and recombination.The variability of genome evolution rate and the selection pressure was identified.Meanwhile,the strains were tested for their pathogenicity by inoculating into four grape cultivars with different levels of disease resistance.The main results are as follows:1.Cross-inoculation experiments showed that the pathogenicity had obvious differences,and the virulence of strains form V.amurensis was significantly lower than other strains from V.vinifera and V.davidii.The sporangium size of isolates from Vitis amurensis was also obviously lower than other populations,suggesting those strains might be a new host-specific cryptic specie.2.Across 95 samples,a total of 1,314,125 high quality SNPs were identified,covering 60.6%of the scaffolds and 88.4%of the genes.Apercent of 8.74%SNPs was found in the coding regions.And for the mutations in those region,non-synonymous mutation accounted for 44.06%,which included SNPs leading to the loss of start-codon,the early termination of encoded protein,and the extension of encoded protein sequence.The results indicated the point mutation is an important driving force for the evolution of P.viticola genome.3.The phylogenetic and PCA analysis of SNPs reveals three distinct P.viticola lineages,each associated with different host plants.4.Genome scans uncovered distinct signatures of selection among populations.127 genes showed population-specific patterns of conservation.Genes that differentiated populations had predicted functions related to metabolism,transmembrane transport and cell wall degrading enzyme,of which 16 were secreted protein and effector.Furthermore,gene presence-absence polymorphism was investigated in the three populations.We observed 147 genes specified present in P.viticola isolates from V.amurensis,and only 1 gene in the V.vinifera and V.davidii,which mainly refers to RNA processing,methylation and signal transduction.The observation of the gene loss and gain events may be related to the adaption of different hosts.These results might have important implications for viticulture,including breeding for resistance and disease management.