Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences

Abstract

Soybean mosaic virus (SMV) of the family Potyviridae is the most devastating virus that infects soybean plants. In this study, we obtained 83 SMV coat protein (CP) sequences from seven provinces in Korea using RT-PCR and Sanger sequencing. Phylogenetic and haplotype analyses revealed eight groups of 83 SMV isolates and a network of 50 SMV haplotypes in Korea. The phylogenetic tree using 305 SMV CP sequences available worldwide revealed 12 clades that were further divided into two groups according to the plant hosts. Recombination rarely occurred in the CP sequences, while negative selection was dominant in the SMV CP sequences. Genetic diversity analyses revealed that plant species had a greater impact on the genetic diversity of SMV CP sequences than geographical origin or location. SMV isolates identified from Pinellia species in China showed the highest genetic diversity. Phylodynamic analysis showed that the SMV isolates between the two Pinellia species diverged in the year 1248. Since the divergence of the first SMV isolate from Glycine max in 1486, major clades for SMV isolates infecting Glycine species seem to have diverged from 1791 to 1886. Taken together, we provide a comprehensive overview of the genetic diversity and divergence of SMV CP sequences.

Keywords: coat protein; haplotype; population; soybean mosaic virus.

Figure 1

Geographical locations of seven provinces and phylogenetic relationship of 83 SMV CP sequences. (A) Geographical locations of seven provinces in Korea in which samples were collected. (B) Maximum likelihood phylogenetic tree of 83 SMV CP nucleotide sequences. The eight identified subgroups are indicated by different colors. Bootstrap values > 75% were indicated.

Figure 2

The composition of 83 SMV CP sequences according to the identified province in each subgroup based on the phylogenetic tree in Figure 1B.

Figure 3

Haplotype network of 83 SMV sequences based on CP sequences. Minimum spanning network was constructed using PopART. The defined eight subgroups were indicated by different colors. Haplotype colors correspond to different provinces (population). The sample sizes in the given haplotype are indicated by the circle size. Each mutation is marked by hatch marks.

Figure 4

Information of 305 SMV CP sequences used for phylogenetic analysis. Pie chart displays the distribution of 305 SMV sequences according to countries (A) and plant host (B).

Figure 5

The phylogenetic relationship of 305 SMV sequences. Maximum likelihood phylogenetic tree of 305 SMV sequences based on CP sequences. The rectangular cladogram of phylogenetic tree can be found in Figure S1. Different background leaf colors represent the 12 recognized clades. Bootstrap values > 75% are indicated. Plant species are indicated as follows. Atractylodes macrocephala (rectangle, orange: orange), Glycine max (circle, red), Glycine soja (circle, green), legume (triangle, orange: red), Passiflora (triangle, orange: green), Passiflora edulis (triangle, orange: blue), Pinellia pedatisecta (star, orange), Pinellia ternate (star, yellow), Strongylodon macrobotrys (rectangle, orange), Uraria crinite (rectangle, violet), Vigna angularis (rectangle, orange: blue), and Vigna unguiculata (rectangle, orange: violet).

Figure 6

Composition of 305 SMV sequences in each clade. The composition of SMV sequences in each clade according to the country (A) and plant host (B) was examined.

Figure 7

Genetic diversity of SMV CP sequences. Nucleotide diversity (Pi) (A) and the average number of segregating sites (θw) (B) of 305 SMV sequences according to country and plant host. “All” indicates all 305 SMV sequences. Four major countries and four major host plants were examined.

Figure 8

Average dN/dS ratios for 305 SMV CP proteins. (A) Distribution of dN/dS ratio for 83 SMV CP proteins from seven different provinces in Korea. (B) Average dN/dS ratio for SMV CP proteins grouped in four countries and four plant hosts, respectively. “All” indicates 305 SMV CP proteins.

Figure 9

Haplotype network of 305 SMV CP sequences. Minimum spanning networks were implemented in PopART. Three regions, defined as region A (A), region B (B), and region C (C), were magnified from the complete haplotype network shown in Figure S3. Haplotype colors correspond to different plant hosts. The sample sizes in the given haplotype are indicated by the circle size. Each mutation is marked by hatch marks. The original network can be found in Figure S3.

Figure 10

Phylogenomic analyses of 305 SMV CP sequences. (A) A maximum likelihood phylogenetic tree with estimated divergence time for 305 SMV CP sequences was created using TreeTime. Individual sequences are indicated by circles and plant hosts are indicated by different colors. Major nodes (branching points) are indicated by the estimated time. (B) Time-resolved tree of clade 1.