Abstract
Plum bark necrosis stem pitting-associated virus (PBNSPaV), a member of the genus Ampelovirus in the family Closteroviridae, infects different Prunus species and has a worldwide distribution. Yet the population structure and genetic diversity of the virus is still unclear. In this study, sequence analyses of a partial heat shock protein 70 homolog (HSP70h) gene and coat protein (CP) gene of PBNSPaV isolates from seven Prunus species grown in China revealed a highly divergent Chinese PBNSPaV population, sharing nucleotide similarities of 73.1–100% with HSP70h gene, and 83.9–98.6% with CP gene. Phylogenetic analysis of HSP70h and CP sequences revealed segregation of global PBNSPaV isolates into four phylo-groups (I–IV), of which two newly identified groups, II and IV, solely comprised Chinese isolates. Complete genome sequences of three PBNSPaV isolates, Pch-WH-1 and Pch-GS-3 from peaches, and Plm-WH-3 from a plum tree, were determined. The three isolates showed overall nucleotide identities of 90.0% (Pch-GS-3) and 96.4% (Pch-WH-1) with the type isolate PL186, and the lowest identity of 70.2–71.2% with isolate Nanjing. For the first time, to the best of our knowledge, we report evidence of significant recombination in the HSP70h gene of PBNSPaV variant Pch2 by using five programs implemented in RDP3; in addition, five codon positions in its CP gene (3, 8, 44, 57, and 88) were identified that appeared to be under positive selection. Collectively, these results indicate a divergent Chinese PBNSPaV population. In addition, our findings provide a foundation for elucidating the epidemiological characteristics of virus population.
Highlights
Plum bark necrosis stem pitting-associated virus (PBNSPaV) is a member of the genus Ampelovirus in the family Closteroviridae [1]
Phylogenetic analysis of the heat shock protein 70 homolog (HSP70h) nucleotide sequences from Chinese isolates determined in the present study, those previously reported by our group, and eight isolates available in GenBank (Table S1 in File S1) using the neighbor-joining method revealed four major groups with strong (100%)
Of the 256 Prunus samples examined in the present study, 56 were found to be infected by PBNSPaV, representing an incidence of 20.3% in stone fruit trees, similar to results obtained for samples collected in Italy [26], but much higher than the incidence identified in other studies [16]
Summary
Plum bark necrosis stem pitting-associated virus (PBNSPaV) is a member of the genus Ampelovirus in the family Closteroviridae [1]. The stem-pitting disease of sweet cherry trees was described in the 1960s in North America [2,3]. Some diseased trees show decline, gummosis, flattening of scaffold branches, severe necrosis of bark tissues, and necrotic pitting on the woody cylinders [18,19]. The plum bark necrosis-stem pitting disease was first confirmed to be grafttransmissible on a Japanese plum cv. The first successful amplification of cDNA fragments, using HSP70h (a homolog of the heat shock protein 70 gene)-degenerate primers for viruses in the family Closteroviridae, identified the virus as a closterovirus, and it was named Plum bark necrosis stem pitting-associated virus (PBNSPaV) [7]. The complete genome sequences of four PBNSPaV isolates have been determined by pyrosequencing, and genome sequence comparison
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