Complete genomic sequence and comparative analysis of rice stripe virus from Sichuan Province, China
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Complete genomic sequence and comparative analysis of rice stripe virus from Sichuan Province, China Gentu Wu 1 & Hao Luo 1 & Guixian Zheng 1 & Xiaoqian Liu 1 & Ling Qing 1 Received: 8 December 2019 / Accepted: 11 April 2020 # Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2020
Abstract Rice stripe virus (RSV) causes viral disease and yield losses in rice. Leaves of rice plants showing yellowing, stripes and curling were collected in Sichuan Province, China and tested for rice strip virus (RSV) by RT-PCR using specific primers. Nine of the nineteen symptomatic samples were positive for RSV. The complete sequence of RSV RNA1 to RNA4 was determined by assembling cDNA fragments obtained from isolate Huid04 in Huidong County, Sichuan Province (GenBank accession Nos. KX611337 to KX611340). Phylogenetic analyses of RNA-dependent RNA polymerase sequences showed a close relationship of RSV isolate Hui0d4 and isolates DaL08 and KunM08 from Yunnan Province, China. This is the first complete genomic sequence of an RSV isolate from Sichuan Province, China. Keywords Rice stripe virus . RT-PCR amplification . Complete genomic sequence . Phylogenetic analysis Rice stripe virus (RSV), the type member of the genus Tenuivirus, is transmitted by the small brown planthopper (Laodelphax striatellus) in a persistent, circulativepropagative manner, and causes rice yield losses in East Asia (Falk and Tsai 1998; Wang et al. 2008; Otuka et al. 2010). The RSV genome contains four single-stranded RNAs named RNA1 to RNA4. All four RNA segments are negative sense molecules with conserved 5′- and 3′-terminal sequences (Barbier et al. 1992; Shimizu et al. 1996; Yao et al. 2012). RNA1 is about 9000 nucleotides (nt) in size and contains a single open reading frame (ORF) encoding a 337-kDa RNAElectronic supplementary material The online version of this article (https://doi.org/10.1007/s42161-020-00558-7) contains supplementary material, which is available to authorized users. * Ling Qing [email protected] Gentu Wu [email protected] Hao Luo [email protected] Guixian Zheng [email protected] Xiaoqian Liu [email protected] 1
College of Plant Protection, Southwest University, Chongqing 400716, China
dependent RNA polymerase (RdRp) in the viral complementary strand (vcRNA). Segments RNA2 to RNA4 have ambisense polarity and two non-overlapping ORFs on opposite strands that are separated by a noncoding intergenic region (IR) that plays critical roles in transcription termination (Zhu et al. 1991; Hamamatsu et al. 1993; Wu et al. 2013). RNA2 encodes a viral RNA silencing suppressor NS2 on the viral sense strand (vRNA) and nonstructural protein NSvc2 on the vcRNA. RNA3 encodes another suppressor of RNA silencing NS3 on the vRNA (Xiong et al. 2009) and a nucleocapsid protein NSvc3 on the vcRNA. RNA4 encodes a disease specific protein NS4 on the vRNA and a movement protein NSvc4 on the vcRNA (Zhu et al. 1992; Xiong et al. 2008; Yuan et al. 2011; Zhang et al. 2012). The complete genomic sequences of RSV isolates from China, Japan, an
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