title: Genetic structure of populations of sugarcane streak mosaic virus in China: Comparison with the populations in India.
abstract: Sugarcane streak mosaic virus (SCSMV) causes mosaic and streak symptoms on sugarcane and sorghum crops, and has a broad host range. SCSMV is a member of the genus Poacevirus in the family Potyviridae.Ten SCSMV isolates were collected from sugarcane plants showing mosaic and streaking in Southern China from 2009-2011. Sequence-based phylogenetic and population genetic analyses were conducted using four partial genomic sequences covering the full genomes. These analyses were used to estimate the subpopulation differentiation and divergence within the Chinese virus population, and were compared with isolates from India. SCSMV-infected sugarcane plants in the field commonly harbor virus quasispecies (mutant cloud), and often have mixed infections with the same virus isolates. Inter- and intra-lineage recombination sites were identified in the protein 1, helper-component proteinase, coat protein and 3' non-coding regions of the Chinese isolates. All the Chinese non-recombinant isolates fell into at least nine lineages, and many clustered with Indian isolates. However, estimates of genetic differentiation and gene flow indicated that the SCSMV populations in China and India are genetically independent. Our genetic study of a poacevirus population in South Asia regions indicates the importance of the evolutionary-based design to control viruses.
authors.affiliation: State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China; Department of Plant Pathology, School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou, 225009 Jiangsu Province, PR China; Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan. Electronic address: hezheng225@163.com.
authors.forename: Zhen
authors.initials: Z
authors.lastname: He
authors.affiliation: Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan; The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima 890-0065, Japan. Electronic address: 14976004@edu.cc.saga-u.ac.jp.
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Yasaka
authors.affiliation: Yunnan Key Laboratory of Genetic Improvement of Sugarcane, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Lingquan East Road No. 363, Kaiyuan, 661600 Yunnan Province, PR China. Electronic address: ynlwf@163.com.
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China. Electronic address: sfli@ippcaas.cn.
authors.forename: Shifang
authors.initials: S
authors.lastname: Li
authors.affiliation: Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan; The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima 890-0065, Japan. Electronic address: ohshimak@cc.saga-u.ac.jp.
authors.forename: Kazusato
authors.initials: K
authors.lastname: Ohshima
mesh_terms: D001483:Base Sequence; D002681:China; D014644:Genetic Variation; D007194:India; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D019176:Potyviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D011995:Recombination, Genetic; D031786:Saccharum / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: Gene flow; Mixed infection; Poacevirus; Population structure; Sugarcane streak mosaic virus