title: Evolution of rice stripe virus.
abstract: Rice stripe virus (RSV) is an insect-borne tenuivirus of economical significance. It is endemic to the rice-growing regions of East Asia and exhibits more genetic diversity in Yunnan Province of China. To gain more insights into the molecular epidemiology and evolution of RSV, recombination analyses were conducted and potential events were detected in each of the four RNA segments of RSV. Bayesian coalescent method was then applied to the time-stamped coding sequences of the CP gene. The nucleotide substitution rate and the divergence time were estimated. Age calculations suggested that the first diversification event of the RSV isolates analyzed might take place in the early 20th century, and RSV has existed in Yunnan long before notice. Surveys of codon usage variation showed that the RSV genes had influences other than mutational bias. In codon choice, RSV conformed to neither vector small brown planthopper nor host rice, although the former exerted a more dominant influence on shaping codon usage pattern of RSV. In addition, CpG dinucleotide deficiency was observed in RSV.
authors.affiliation: College of Life Science, Shandong Normal University, Jinan 250014, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
authors.forename: Mei
authors.initials: M
authors.lastname: He
authors.affiliation: College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China.
authors.forename: Sheng-Yu
authors.initials: SY
authors.lastname: Guan
authors.affiliation: College of Life Science, Shandong Normal University, Jinan 250014, China. Electronic address: hchqiang@sdnu.edu.cn.
authors.forename: Cheng-Qiang
authors.initials: CQ
authors.lastname: He
mesh_terms: D001499:Bayes Theorem; D002681:China; D003062:Codon; D019143:Evolution, Molecular; D014644:Genetic Variation; D012275:Oryza / Q000821:virology; D010802:Phylogeny; D029364:Tenuivirus / Q000145:classification* / Q000235:genetics
chemical_list: D003062:Codon
keywords: Codon usage bias; CpG dinucleotide; Divergence; RSV; Recombination