The Complete Genome Sequence of Southern rice black-streaked dwarf virus Isolated from Vietnam

Abstract

Faculty of Agriculture Forestry Fisheries, Vinh University, Vinh city, Nghe An province 42000, Vietnam(Received on March 21, 2012; Revised on July 3, 2012; Accepted on July 11, 2012)We determined the complete genome sequence of aVietnamese isolate of Southern rice black-streaked dwarfvirus (SRBSDV). Whole genome comparisons andphylogenetic analysis showed that the genome of theVietnamese isolate shared high nucleotide sequenceidentities of over 97.5% with those of the reportedChinese isolates, confirming a common origin of them.Moreover, the greatest divergence between differentSRBSDV isolates was found in the segments S1, S3, S4and S6, which differs from the sequence alignmentresults between SRBSDV and Rice black streaked dwarfvirus (RBSDV), implying that SRBSDV evolved in aunique way independent of RBSDV. This is the firstreport of a complete nucleotide sequence of SRBSDVfrom Vietnam and our data provides new clues forfurther understanding of molecular variation andepidemiology of SRBSDV in Southeast Asia.Keywords : phylogenetic analysis, sequence, Southern riceblack-streaked dwarf virus, vietnamese isolate Southern rice black-streaked dwarf virus (SRBSDV) isproposed to be a novel member of the Fijivirus group 2 inthe family Reoviridae (Attoui, 2011; Zhang et al., 2008;Zhou et al., 2008). The double-stranded (dsRNA) ofSRBSDV contains 10 segments (S1 to S10), which werenamed in order of decreasing molecular weight (Zhou et al.,2008). SRBSDV was first observed in Yangxi county,Guangdong province in China in 2001. From then on, thisdisease became one of the most serious viral diseases ofrice in southern and central China, causing severe losses inrice production (Wang et al., 2010; Zhou et al., 2010). In2008, SRBSDV was also detected in maize plants innorthern China (Yin et al., 2011). In 2010, the occurrence ofSRBSDV disease was firstly reported in rice fields in theKumamoto Prefecture of Japan (Choi, 2010). In 2009, seriousviral rice disease occurred in many northern provinces ofVietnam, expanding to a total of 5506 hectares. Of this area,the yields of approximately 3510 hectares were totally lost.The causal agent of the rice dwarf disease in the north ofVietnam has also been identified as SRBSDV (Cuong et al.,2009; Hoang et al., 2011). Further investigation suggestedthat the outbreak of SRBSDV in Vietnam was associatedwith rising populations of the white-backed plant hopper(Sogatella furcifera), which is the major vector of SRBSDV(Cuong et al., 2009; Zhou et al., 2008). As planthoppers areconstantly displaced by wind currents, the spread of thevirus diseases they carry will be inevitable.Symptoms of SRBSDV infection vary depending on thecrop age when infected. Characteristic symptoms includedark-green and wrinkled leaves, incomplete tassel, tumor-like protrusions ending in small enations, tiller formation onthe upper parts, up-growing rootlets, and in particular thepresence of white to black waxy galls along the major veinsof the leaves and culms (Wang et al., 2012; Zhou et al.,2008; Zhou et al., 2010). Up to now, the complete genome sequence of SRBSDVhad been obtained only for three isolates, which originatedfrom Guangdong (GD), Hainan (HN) and Hubei (HB)provinces of China, respectively (Wang et al., 2010). Asonly partial sequences of segments 4 and 10 from severalVietnamese isolates were investigated and the S10 segmentwas very conserved among different isolates (Cuong et al.,2009; Hoang et al., 2011), more information about thegenome sequence of an SRBSDV isolate from Vietnamwill further characterize the geographic and molecularvariation of this virus, thus facilitating control and preven-tion of this disease in Southeast Asia.Viral genomic dsRNAs were extracted directly fromnaturally infected field-grown rice plants from Thua ThienHue province in central Vietnam using the method describ-ed previously (Dodds et al., 1984). Primers for cloningsegments S1 to S10 of Vietnamese isolate were designed toobtain the full length sequence of each genome segmentbased on the previously reported SRBSDV sequencesavailable in GenBank of NCBI (Wang et al., 2010). Twostep RT-PCR was employed to clone cDNA fragments of