title: Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions.
abstract: The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.
authors.affiliation: College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China.|Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Hunan, 410128, China.
authors.forename: Maoyan
authors.initials: M
authors.lastname: Liu
authors.affiliation: College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China.|Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Hunan, 410128, China.
authors.forename: Xiangning
authors.initials: X
authors.lastname: Liu
authors.affiliation: College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China.|Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50010, USA.
authors.forename: Xun
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Hunan, 410125, China.
authors.forename: Deyong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China. daily@hunau.net.|Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Hunan, 410128, China. daily@hunau.net.
authors.forename: Liangyin
authors.initials: L
authors.lastname: Dai
authors.affiliation: College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China. tangqianjun78@163.com.|Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Hunan, 410128, China. tangqianjun78@163.com.|Virus Research Institute, Hunan Agricultural University, Hunan, 410128, China. tangqianjun78@163.com.
authors.forename: Qianjun
authors.initials: Q
authors.lastname: Tang
mesh_terms: D002212:Capsicum / Q000821:virology*; D002681:China; D016000:Cluster Analysis; D019143:Evolution, Molecular; D023061:Gene Order; D040961:Genetic Drift; D016679:Genome, Viral; D006801:Humans; D052679:Luteoviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins
keywords: Complete genome; Deep sequencing; Molecular evolution; Pepper vein yellows virus