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Genetic structure of populations of Sugarcane streak mosaic virus in China and comparison with isolates from India

Zhen He;Ryosuke Yasaka;Shifang Li;Kazusato Ohshima

  Sugarcane streak mosaic virus(SCSMV) causes mosaic and streak symptoms on infected plants,and is one of the most important viruses infecting sugarcane and sorghum crops.SCSMV is a member of the genus Poacevirus in the family Potyviridae.Ten SCSMV isolates were collected from sugarcane plants showing mosaicism 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 P1,HCPro,CP,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 such studies for the science-based design of potential virus control strategies.……