Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Abstract

Broad bean wilt virus 2 (BBWV-2), which belongs to the genus Fabavirus of the family Secoviridae, is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previously, only limited reports have shown the genetic variation of BBWV2. Meanwhile, the detailed evolutionary changes, synonymous codon usage bias and host adaptation of this virus are largely unclear. Here, we performed comprehensive analyses of the phylodynamics, reassortment, composition bias and codon usage pattern of BBWV2 using forty-two complete genome sequences of BBWV-2 isolates together with two other full-length RNA1 sequences and six full-length RNA2 sequences. Both recombination and reassortment had a significant influence on the genomic evolution of BBWV2. Through phylogenetic analysis we detected three and four lineages based on the ORF1 and ORF2 nonrecombinant sequences, respectively. The evolutionary rates of the two BBWV2 ORF coding sequences were 8.895 × 10^-4 and 4.560 × 10^-4 subs/site/year, respectively. We found a relatively conserved and stable genomic composition with a lower codon usage choice in the two BBWV2 protein coding sequences. ENC-plot and neutrality plot analyses showed that natural selection is the key factor shaping the codon usage pattern of BBWV2. Strong correlations between BBWV2 and broad bean and pepper were observed from similarity index (SiD), codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses. Our study is the first to evaluate the phylodynamics, codon usage patterns and adaptive evolution of a fabavirus, and our results may be useful for the understanding of the origin of this virus.

Keywords: broad bean wilt virus 2; codon usage pattern; host adaptation; natural selection.

Figure 1

The maximum-likelihood (ML) trees calculated from the ORF1 (A) and ORF2 (B) sequences of nonrecombinant broad bean wilt virus 2. Numbers at each node indicate the percentage of bootstrap samples in the NJ and ML trees. The horizontal branch length is drawn to scale with the bar indicating 0.05 nt replacements per site.

Figure 1

The maximum-likelihood (ML) trees calculated from the ORF1 (A) and ORF2 (B) sequences of nonrecombinant broad bean wilt virus 2. Numbers at each node indicate the percentage of bootstrap samples in the NJ and ML trees. The horizontal branch length is drawn to scale with the bar indicating 0.05 nt replacements per site.

Figure 2

Graphs comparing patristic distances in pairs of maximum-likelihood trees based on the ORF1 and ORF2 sequences of nonrecombinant broad bean wilt virus 2. (A) Graphs comparing patristic distances; (B) correlation coefficient of ORF1 and ORF2.

Figure 3

The relative and cumulative inertia of the 35 axes from a COA of the RSCU values based on the ORF1 (A) and ORF2 (B) sequences of broad bean wilt virus 2. PCA based on the RSCU values of the ORF1 (C) and ORF2 (D) sequences of broad bean wilt virus 2. The broad bean pepper, spinach and yam hosts are showed in green, blue, purple and red dots, respectively.

Figure 4

ENC-plot analysis of ORF1 (A) and ORF2 (B) sequences of broad bean wilt virus 2, with ENC against the GC3s of different hosts. The orange dotted line represents the standard curve when the codon usage bias is determined by the GC3s composition only. The broad bean pepper, spinach and yam hosts are showed in green, blue, purple and red dots, respectively.

Figure 5

Neutrality plot analysis of GC3 against GC12 for the ORF1 (A) and ORF2 (B) sequences of broad bean wilt virus 2. The broad bean, pepper, spinach and yam hosts are represented in green, blue, purple and red dots, respectively.

Figure 6

Parity plot showing the presence of AT bias [A3%/(A3% + T3%)] and GC bias [G3%/(G3% + C3%)] for the ORF1 (A) and ORF2 (B) sequences of broad bean wilt virus 2. The center of the plot, where the value of both coordinates is 0.5, indicates the place where there is no bias in mutation or selection rates. The broad bean pepper, spinach and yam hosts are represented in green, blue, purple and red dots, respectively.

Figure 7

The CAI analysis and RCDI analysis of the ORF1 (A) and ORF2 (B) sequences of broad bean wilt virus 2 in relation to the natural hosts. The x-axis represents the sequences identified in different hosts.

Figure 8

The SiD analysis of the ORF1 (A) and ORF2 (B) sequences of broad bean wilt virus 2 in relation to the natural hosts. The broad bean pepper, spinach and yam hosts are showed in light orange, green, purple and yellow column, respectively. The x-axis represents the sequences identified in different hosts.