Evolution and Phylogeny of Soybean Mosaic Virus Based on 143 Complete Genomes

Abstract

Soybean mosaic virus (SMV) of the genus Potyvirus 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 Pinellia and Atractylodes 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.

Investigating Variability in Viral Presence and Abundance across Soybean Seed Development Stages Using Transcriptome Analysis

“…We meticulously reviewed our data analysis procedures, including the parameters for de novo transcriptome assembly, to rule out potential issues. In this pursuit, we replicated the analyses performed in our prior studies, which successfully generated complete viral genomes for SMV, CMV, and BBWV2 [3,5,31]. The outcome of this comparative analysis affirmed the integrity of our data analysis process.…”

“…Among these, SMV was the most prevalent virus in both the Glycine max (GM) and Glycine soja (GS) cultivars, with a higher number of contigs detected in GS. As previously reported, SMV was identified as the predominant virus that infects Glycine species [ 3 , 5 , 6 ]. Furthermore, it is well-established that SMV can be transmitted through seeds [ 22 ].…”

“…Soybean mosaic virus (SMV) is a single-stranded positive-sense RNA virus belonging to the genus Potyvirus in the family Potyviridae and is regarded as one of the most significant viral pathogens that impacts soybean on a global scale [ 5 , 6 ]. SMV infects a wide range of soybean cultivars and wild relatives, leading to severe yield losses and significant reductions in seed quality [ 7 ].…”

Molecular Genetics Enhances Plant Breeding

“…Meanwhile, marker-assisted pre-breeding is underdoing a transformation from the method of classically screening crop genepools to the assessment of their associated antagonistic biotic agents. For example, Choi et al [ 7 ] elucidated the molecular phylogenetic origin of seven strains of soybean mosaic virus (SMV) that had been sampled from 150 Glycine max L. accessions. The use of RNA-seq and 143 SMV available genomes enabled concluding that recombination and plant hosts drive the genetic diversity of SMV.…”

“…For original datasets, please refer to the published articles [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ] within the second Special Issue of IJMS on “Molecular Genetics and Plant Breeding 2.0” ( , as accessed on 6 June 2023).…”