JIA-2019-11

Journal of Integrative Agriculture 2019, 18(11): 2664–2667 SHORT COMMUNICATION Available online at www.sciencedirect.com ScienceDirect First detection and complete genome of Soybean chlorotic mottle virus naturally infecting soybean in China by deep sequencing HU Qian-qian 1 , LIU Xue-jian 1 , HAN Xue-dong 1 , LIU Yong 2 , JIANG Jun-xi 3 , XIE Yan 1 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R.China 2 Hunan Plant Protection Institute, Changsha 410125, P.R.China 3 College of Agriculture, Jiangxi Agricultural University, Nanchang 330000, P.R.China Abstract Soybean chlorotic mottle virus (SbCMV) was first detected from soybean plants in Jiangxi Province of China by high throughput sequencing and was confirmed by PCR. The complete nucleotide sequence of NC113 was determined to be 8 210 nucleotides, and shared the highest similarity (91.7%) with sequences of SbCMV that was only reported in Japan. It encodes nine putative open reading frames (ORFs Ia, Ib and II–VIII), and contains a large intergenic region located at nucleotide 5 976–6 512 between ORFs VI and VII. Sequence analysis and phylogenetic tree indicated that NC113 is an isolate of SbCMV, and is more related to the soymoviruses Blueberry red ringspot virus (BRRSV), Peanut chlorotic streak virus (PCSV) and Cestrum yellow leaf curling virus (CmYLCV) than to other representative members in the Caulimoviridae family. Field survey of 472 legume plants from Jiangxi and Zhejiang provinces showed SbCMV was only detected from soybean in Nanchang City with a low incidence rate. This is the first report of Soybean chlorotic mottle virus identified in China. Keywords: Soybean chlorotic mottle virus , Soymovirus , genome sequence, sequence analysis (Hibi et al . 1986; Verver et al . 1987; Geering and Hull 2012). The three members of Soymovirus , Blueberry red ringspot virus (BRRSV), Peanut chlorotic streak virus (PCSV) and SbCMV, and the tentative species Cestrum yellow leaf curling virus (CmYLCV) can be distinguished from their closest relatives in the genus Caulimovirus by the presence of three open reading frames (ORFs Ib, II and III) between the movement protein and the coat protein instead of two ORFs (ORFs II and III) (Hasegawa et al . 1989; Mushegian et al . 1995; Glasheen et al . 2002; Stavolone et al . 2003). SbCMV encodes nine ORFs and one large intergenic region (IR). ORF Ia is the movement protein, ORF II can display self-interaction and is essential for SbCMV infectivity, the products of ORFs III, IV, V and VI are predicted to encode the virion-associated protein, the coat protein, the polymerase polyprotein (reverse transcriptase and RNaseH enzymatic activities) and the translation transactivator, respectively, Received 6 November, 2018 Accepted 18 March, 2019 HU Qian-qian, E-mail: yimonu@163.com; Correspondence XIE Yan, Tel: +86-571-88982677, E-mail: xiey@zju.edu.cn © 2019 CAAS. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/) . doi: 10.1016/S2095-3119(19)62665-1 1. Introduction Soybean chlorotic mottle virus (SbCMV), the type species of the genus Soymovirus in the family Caulimoviridae , contains a single molecule of non-covalently closed circular double-stranded DNA molecule ranging from 8.1 to 8.3 kb and their isometric particles are about 50 nm in diameter