Molecular Evolution Of Sugarcane Streak Mosaic Virus And Sorshum Mosaic Virus

Sugarcane mosaic disease (SMD), which is widespread across the world in areas where sugarcaneis cultivated, is considered to be an important disease in this crop. SMD is also distributed widely inYunnan Province, which is the second largest sugarcane producing region in China. However, the exactidentity of the pathogens responsible and the distribution of the disease in this area are currentlyunknown. Sugarcane mosaic virus (SCMV)(family Potyviridae; genus Potyvirus), Sorghum mosaicvirus (SrMV)(family Potyviridae; genus Potyvirus) and Sugarcane streak mosaic virus (SCSMV)(family Potyviridae; genus Poacevirus) are the predominant causative agents of SMD; however fewstudies on the molecular evolution of SCSMV and SrMV have been reported to date. In this study, wesurveyed the occurrence and distribution of the pathogens causing SMD in Yunnan Province in Chinaand analyzed the molecular evolution of SCSMV and SrMV.During2009–2012,324samples of sugarcane displaying the symptoms of mosaic disease werecollected from sugarcane cultivated areas in Yunnan Province and the National Nursery for SugarcaneGermplasm Resources and analyzed by RT-PCR. SrMV, SCSMV and SCMV were identified as thecausal agents of SMD in these samples. SrMV was the predominant pathogen responsible for SMD,accounting for up to34%of the affected cultivars or regions. SCSMV was also shown to be animportant SMD pathogen in Yunnan Province, accounting for up to50%of the infections in samplesfrom the Yuanjing Prefecture. SCMV was the least dominant of the three viruses, although it also couldup to41%in fewer sugarcane cultivar. Mixed infections were commonly detected in some sugarcanehosts, especially coinfections of SrMV with SCSMV or SCMV. Coinfections of SCSMV and SCMVwere also identified in a few hosts, although mixed infections with all three viruses in the samesugarcane plant were not identified. Here, we report for the first time the occurrence and distribution ofSCSMV in sugarcane growing areas in China.Thirty-two SCSMV positive samples were selected from sugarcane cultivated areas in YunnanProvince and the National Nursery for Sugarcane Germplasm Resources and the genomic sequenceswere determined. The molecular evolution of SCSMV obtained in this study and sequences obtainedfrom GenBank were analyzed focusing on the P1, HC-Pro, NIa and CP protein encoding regions. Ourresults showed that mutation, negative selection and genetic drift (founder effecter) were the underlyingdrivers of the dynamics of the molecular evolution of SCSMV; however, recombination did notsignificantly affect SCSMV evolution. Two genetically independent populations distributed in Chinaand India were formed by different SCSMV isolates, although we could not confirm the origin of thetwo populations. Furthermore, the SCSMV forming the Chinese and Indian populations was in suddenexpansion.The molecular evolution of SrMV was analyzed by focusing on the P1and CP protein encodingregions located in the5’ and3’ terminal regions of the SrMV genome. Phylogenetic analysis suggested that all SrMV isolates obtained in this study and those obtained from GenBank were clustered into twogroups according to the P1and CP protein encoding regions. High genetic diversity was found betweenthe two groups, with average genetic distances of up to61%and23%, respectively, which complieswith the criterion used to define different species of the Potyvirus genus. Therefore, we speculated thatthe two groups of SrMV represent two new viruses, the molecular evolution of which waspredominantly due to negative selection and genetic drift (founder effecter) rather than recombination.These data indicate that Yunnan Province is a center of genetic diversity for SrMV.