De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data
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 av...
| मुख्य लेखकों: | , , , , , , , |
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| स्वरूप: | लेख |
| भाषा: | English |
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Hanrimwon Publishing Company
2017-10-01
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| श्रृंखला: | The Plant Pathology Journal |
| विषय: | |
| ऑनलाइन पहुंच: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624490 |
| _version_ | 1829118041268420608 |
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| author | Yeonhwa Jo Hoseong Choi Miah Bae Sang-Min Kim Sun-Lim Kim Bong Choon Lee Won Kyong Cho Kook-Hyung Kim |
| author_facet | Yeonhwa Jo Hoseong Choi Miah Bae Sang-Min Kim Sun-Lim Kim Bong Choon Lee Won Kyong Cho Kook-Hyung Kim |
| author_sort | Yeonhwa Jo |
| collection | DOAJ |
| description | 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 de novo 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. |
| first_indexed | 2024-12-13T10:13:18Z |
| format | Article |
| id | doaj.art-b51f18b1eea74213aa9e5c1c4150c9e9 |
| institution | Directory Open Access Journal |
| issn | 1598-2254 |
| language | English |
| last_indexed | 2024-12-13T10:13:18Z |
| publishDate | 2017-10-01 |
| publisher | Hanrimwon Publishing Company |
| record_format | Article |
| series | The Plant Pathology Journal |
| spelling | doaj.art-b51f18b1eea74213aa9e5c1c4150c9e92022-12-21T23:51:22ZengHanrimwon Publishing CompanyThe Plant Pathology Journal1598-22542017-10-0133547848710.5423/PPJ.OA.03.2017.0060PPJ.OA.03.2017.0060De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome DataYeonhwa Jo0Hoseong Choi1Miah Bae2Sang-Min Kim3Sun-Lim Kim4Bong Choon Lee5Won Kyong Cho6Kook-Hyung Kim7Department 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, KoreaDepartment 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, KoreaDepartment 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, KoreaCrop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365, KoreaCrop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365, KoreaCrop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365, KoreaDepartment 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, KoreaDepartment 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, KoreaSoybean 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 de novo 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.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624490de novo genome assemblysingle nucleotide variationsoybean mosaic virus |
| spellingShingle | Yeonhwa Jo Hoseong Choi Miah Bae Sang-Min Kim Sun-Lim Kim Bong Choon Lee Won Kyong Cho Kook-Hyung Kim De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data The Plant Pathology Journal de novo genome assembly single nucleotide variation soybean mosaic virus |
| title | De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data |
| title_full | De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data |
| title_fullStr | De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data |
| title_full_unstemmed | De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data |
| title_short | De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data |
| title_sort | de novo genome assembly and single nucleotide variations for soybean mosaic virus using soybean seed transcriptome data |
| topic | de novo genome assembly single nucleotide variation soybean mosaic virus |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624490 |
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