| Rice stripe disease caused by Rice stripe virus (RSV) has a trend of higher epidemiology in China in last two years. This disease has broken out in Jiangsu and Henan provinces, and also caused severe damage to rice production in Yunnan, Shandong, Beijing, Liaoning, Fujian, Zhejiang and Shanghai provinces. Broad distribution and broad host range of RSV resulted into likely rich virus genetic diversity. Here we analyzed the population genetic diversity of NS2, coat protein (CP) and disease-specific protein (SP) genes of RSV isolates from outbreak sites at Jiangsu and Henan provinces, as well as from endemic sites at Yunnan, Shandong, Beijing, Liaoning, Fujian, Zhejiang and Shanghai provinces, in order to further discuss the molecular variability and evolution mechanisms of RSV.The population structure and genetic variation of NS2, CP and SP genes encoded by RNA2, RNA 3 or RNA 4 of RSV within and between eighty isolates collected from 9 different provinces in China were estimated by single-strand conformation polymorphism (SSCP) and sequence analysis. The results showed that Chinese RSV isolates analyzed here were composed of populations each of which contained a majority haplotype and a few haplotypes in a very low frequency. The intra-isolate genetic diversity also consisted of one major variant and other sequence variants of lower frequencies. These results suggested that population structure and genetic diversity of Chinese RSV was predicted by the quasispecies structure for RNA viruses. From the data of the dN/ds ratio (0.1975 for NS2 gene, 0.2866 for CP gene and 0.3410 for NS3 gene) and genetic diversity (0.021 for NS2 gene, 0.033 for CP gene and 0.037 for SP gene), we can concluded that NS2 gene was the most conserved and lowest diversity compared to CP and SP genes, and SP gene was the most variable among the three genes. These results indicated that different negative selection constraints imposed by different functional regions might have maintained different conserved regions of these three genes. Sequence analysis of the three genes showed that these isolates and two Japanese isolates could be divided into two diverged groups. A part of isolates collected from Yunnan province formed one group and the other group contained the rest of the RSV isolates. Phylogenetic studies based on the sequences confirmed the geographical isolation of RSV virus population, but showed that gene flow might occur between populations. However, In terms of the effects of hosts on the population structure of RSV, the finding that different isolates from different rice varieties and three different host species of wheat, barely and cockspur grass had the same SSCP patterns suggested that different host plants did not contribute to differentiation of the virus population, as observed with other plant viruses. This was the first report about population genetic structure and genetic diversity of negative-sense RNA plant viruses.The complete nucleotide (nts) sequences of RNA 1-4 of two isolates of RSV,isolated from Chuxiong (YCX1), Yunnan Province, and Hongze (JHZ), Jiangsu Province, were determined. RNA1-4 of YCX1 isolate were 8970 nts (RNA1), 3506 nts (RNA2), 2489 nts (RNA3) and 2137 nts (RNA4) in length, respectively; RNA1-4 of JHZ isolate were 8970 (RNA1), 3514 nts (RNA2), 2509 nts (RNA3) and 2157 nts (RNA4) in length, respectively. Compared with the complete nucleotide sequences of RNA1-4 of T isolate from Japan, the numbers of nucleotides in the terminal untranslated regions (UTR), intergenic regions (IRs) and open reading frames (ORF) were identical between JHZ and T isolates except for a deletion of 5 nt in length in the RNA3 IR of JHZ isolate. The most conserved regions of RNA1-4 among these three isolates located in 5' and 3' UTR, suggesting that these regions played a very important role in transcription and replication of viral genome. The most variable regions of these three isolates located in the IRs of RNA2-4, sequence comparison showed that there were deletion and insert sequences in the IRs, computer-a...
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