Evolution of rice stripe virus

[Display omitted] •Recombination events were detected in each RNA segment of RSV.•The primary bifurcation event of RSV might take place in the early 1900s.•RSV has existed in Yunnan Province of China long before notice.•In codon choice, RSV complies with neither insect vector nor plant host.•RSV exhibits CpG dinucleotide deficiency. 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.