Table_5_Geographic Distribution and Genetic Diversity of Rice Stripe Mosaic Virus in Southern China.DOCX

Rice stripe mosaic virus (RSMV) transmitted by the leafhopper Recilia dorsalis is a tentative new species in the genus Cytorhabdovirus identified recently in South China. To explore its geographic distribution and genetic diversity, field investigation and viral whole-genome sequencing were conducted in this study. The results indicated that RSMV was present in the rice samples collected across southern China. Twelve representative samples from different geographical regions were selected for viral whole-genome sequencing and the viral genome variation was analyzed in combination with a previously reported RSMV isolate. Identity analysis showed that the genome sequences of 13 RSMV isolates were highly conserved with nucleotide identities over 99.4%. There was a strong negative selection pressure during the evolution of RSMV with more transitions (72.08%) than transversions (27.92%) found between the RSMV isolates. Among the seven genes encoded by RSMV, the P gene was the most variable, followed by N, M, L, and G; the P3 and P6 amino acid sequences were not found to be mutated and no mutations were found in the non-coding region. A phylogenetic tree based on the RSMV whole-genome nucleotide sequences revealed that all RSMV isolates clustered in two groups based on geographical origin. Notably, the L proteins of the Guangxi and Hainan isolates had five and one specific amino acid sites, respectively, suggesting that the L gene has undergone environmental adaptive variation during the dispersal of RSMV.

水稻条纹花叶病毒（Rice stripe mosaic virus, RSMV）由黑尾叶蝉（Recilia dorsalis）传播，是近期在中国南方发现的细胞质弹状病毒属（Cytorhabdovirus）暂定新种。为探究该病毒的地理分布与遗传多样性，本研究开展了田间调查与病毒全基因组测序工作。结果显示，采集自中国南方各地的水稻样本中均检测到RSMV。本研究选取来自不同地理区域的12份代表性样本进行病毒全基因组测序，并结合已报道的1株RSMV分离物，对病毒基因组变异情况展开分析。序列一致性分析结果表明，13株RSMV分离物的基因组序列高度保守，核苷酸一致性均高于99.4%。RSMV进化过程中存在较强的负选择压力，分离物间的碱基转换（72.08%）显著多于颠换（27.92%）。在RSMV编码的7个基因中，P基因变异程度最高，依次为N、M、L、G基因；未检测到P3与P6蛋白的氨基酸序列发生突变，非编码区域亦未发现突变位点。基于RSMV全基因组核苷酸序列构建的系统发育树显示，所有RSMV分离物可按照地理来源划分为两个聚类群。值得注意的是，广西与海南分离物的L蛋白分别存在5个和1个特异性氨基酸位点，这表明L基因在RSMV传播扩散过程中发生了环境适应性变异。