Journal of Integrative Agriculture ›› 2014, Vol. 13 ›› Issue (10): 2184-2195.DOI: 10.1016/S2095-3119(13)60653-X

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Genetic Diversity of Chinese Soybean mosaic virus Strains and Their Relationships with Other Plant Potyviruses Based on P3 Gene Sequences

 YANG Qing-hua, LI Kai, ZHI Hai-jian , GAI Jun-yi   

  1. Soybean Research Institute, Nanjing Agricultural University/National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology, Nanjing 210095, P.R.China
  • 收稿日期:2013-03-20 出版日期:2014-10-01 发布日期:2014-10-10
  • 通讯作者: GAI Jun-yi, Tel/Fax: +86-25-84395405, E-mail: sri@njau.edu.cn
  • 作者简介:YANG Qing-hua, E-mail: tsingyang2009@163.com; LI Kai, E-mail: kail@njau.edu.cn; These authors contributed equally to this study.
  • 基金资助:

    This work was supported by the National Natural Science Foundation of China (30671266, 31101164), the National Basic Research Program of China (2006CB101708, 2009CB118404), the National 863 Program of China (2006AA100104), the 111 Project from Ministry of Education of China (B08025) and the Youth Science and Technology Innovation Foundation of Nanjing Agriculture University, China (KJ2010002).

Genetic Diversity of Chinese Soybean mosaic virus Strains and Their Relationships with Other Plant Potyviruses Based on P3 Gene Sequences

 YANG Qing-hua, LI Kai, ZHI Hai-jian , GAI Jun-yi   

  1. Soybean Research Institute, Nanjing Agricultural University/National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology, Nanjing 210095, P.R.China
  • Received:2013-03-20 Online:2014-10-01 Published:2014-10-10
  • Contact: GAI Jun-yi, Tel/Fax: +86-25-84395405, E-mail: sri@njau.edu.cn
  • About author:YANG Qing-hua, E-mail: tsingyang2009@163.com; LI Kai, E-mail: kail@njau.edu.cn; These authors contributed equally to this study.
  • Supported by:

    This work was supported by the National Natural Science Foundation of China (30671266, 31101164), the National Basic Research Program of China (2006CB101708, 2009CB118404), the National 863 Program of China (2006AA100104), the 111 Project from Ministry of Education of China (B08025) and the Youth Science and Technology Innovation Foundation of Nanjing Agriculture University, China (KJ2010002).

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摘要： Soybean mosaic virus (SMV), a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1 041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide (NT) sequence identities and 95.1-100% amino acid (AA) sequence identities. The P3 coding regions of the 16 SMV isolates share high identities (92.4-98.9% NT and 96.0-100% AA) with the reported Korean isolates, followed by the USA isolates (88.5-97.9% NT and 91.4-98.6% AA), and share low identities (80.5-85.2% NT and 82.1-84.7% AA) with the reported HZ1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus (WMV), with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.

关键词: Soybean mosaic virus , Potyvirus , P3 gene , homology analysis , phylogenetic tree , multiple sequence alignment

Abstract: Soybean mosaic virus (SMV), a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1 041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide (NT) sequence identities and 95.1-100% amino acid (AA) sequence identities. The P3 coding regions of the 16 SMV isolates share high identities (92.4-98.9% NT and 96.0-100% AA) with the reported Korean isolates, followed by the USA isolates (88.5-97.9% NT and 91.4-98.6% AA), and share low identities (80.5-85.2% NT and 82.1-84.7% AA) with the reported HZ1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus (WMV), with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.

Key words: Soybean mosaic virus , Potyvirus , P3 gene , homology analysis , phylogenetic tree , multiple sequence alignment