Jo Yeonhwa, Choi Hoseong, Bae Miah, Kim Sang-Min, Kim Sun-Lim, Lee Bong Choon, Cho Won Kyong, Kim Kook-Hyung
Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
Crop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365, Korea.
Plant Pathol J. 2017 Oct;33(5):478-487. doi: 10.5423/PPJ.OA.03.2017.0060. Epub 2017 Oct 1.
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.
大豆是世界上最重要的豆科作物。大豆中的几种病害会导致主要大豆生产国的产量严重损失。此外，大豆还会受到多种病毒的感染。最近，我们利用现有的大豆转录组数据进行了大规模筛选，以鉴定感染大豆的病毒。在筛选出的转录组中，一个用于大豆种子发育分析的大豆转录组包含几个与病毒相关的序列。在本研究中，我们通过转录组组装和比对搜索鉴定出了包括大豆花叶病毒（SMV）在内的五种感染大豆的病毒。我们利用转录组数据组装了一个近乎完整的SMV中国株系的共有基因组序列。基于系统发育分析，SMV中国株系的共有基因组序列与来自韩国的SMV分离株密切相关。我们检测了大豆种子转录组中SMV的单核苷酸变异（SNV），共发现780个SNV，它们均匀分布在SMV基因组上。其中，C-U、U-C、A-G和G-A这四种SNV较为常见。这一结果证明了SMV基因组的准种变异。综上所述，本研究利用大豆转录组数据进行了生物信息学分析以鉴定病毒。此外，我们还展示了大豆转录组数据在病毒基因组组装和SNV分析中的应用。
