Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea.
College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea.
Int J Mol Sci. 2022 Dec 20;24(1):22. doi: 10.3390/ijms24010022.
(SMV) of the genus is an important virus in cultivated soybeans. Here, we obtained 7 SMV genomes from soybean germplasms using RNA sequencing and conducted a comprehensive evolutionary and phylogenetic study of 143 SMV genomes derived from 10 plant species and 12 countries. The phylogenetic tree we constructed using coding DNA sequences revealed the existence of nine clades of SMV isolates/strains. Recombination analysis revealed 76 recombinant events and 141 recombinants in total. Clades 1 and 3 contain the most common SMV pathotypes, including G1 through G7, which are distributed worldwide. Clade 2 includes several Chinese SMV pathotypes. The SMV isolates were further divided into two groups. The SMV isolates in the first group, including clades 8 and 9, were identified from and species, whereas those in the second group (clades 1 through 7) were mostly found in cultivated soybeans. The SMV polyprotein undergoes positive selection, whereas most mature proteins, except for the P1 protein, undergo negative selection. The P1 protein of SMV isolates in group 1 may be highly correlated with host adaptation. This study provides strong evidence that recombination and plant hosts are powerful forces driving the genetic diversity of the SMV genome.
属的 SMV 是栽培大豆中的重要病毒。在这里，我们使用 RNA 测序从大豆种质中获得了 7 个 SMV 基因组，并对来自 10 种植物和 12 个国家的 143 个 SMV 基因组进行了全面的进化和系统发育研究。我们使用编码 DNA 序列构建的系统发育树揭示了 SMV 分离株/株系的 9 个进化枝的存在。重组分析总共揭示了 76 个重组事件和 141 个重组体。进化枝 1 和 3 包含最常见的 SMV 致病型，包括分布在全球的 G1 到 G7。进化枝 2 包括几种中国的 SMV 致病型。SMV 分离株进一步分为两组。第一组 SMV 分离株，包括进化枝 8 和 9，来自 和 物种，而第二组（进化枝 1 到 7）主要存在于栽培大豆中。SMV 多蛋白经历正选择，而大多数成熟蛋白，除 P1 蛋白外，经历负选择。组 1 中 SMV 分离株的 P1 蛋白可能与宿主适应性高度相关。本研究提供了强有力的证据，证明重组和植物宿主是驱动 SMV 基因组遗传多样性的强大力量。
