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.

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

“…In this paper, the average values of NYSV, NDV and NLSYV were 55.78, 55.62 and 54.79, respectively, indicating that codon bias was low. The low codon usage bias was also observed in the sugarcane mosaic virus (SCMV), potato virus M (PVM), broad bean wilt virus 2 (BBWV2) and papaya ringspot virus (PRSV) [ 48 , 49 , 50 , 51 ]. Studies have found that low codon usage bias reduces the competition for the synthesis mechanism between viruses and hosts, which is conducive to the expression of viral genes in host cells.…”

Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype

“…According to a recent study ( He et al, 2021 ), we employed Codon W software (version 1.4.2) to compute the frequencies of A, T, C, and G at the third positions (A3s, U3s, G3s, C3s) in the synonymous codons. Meanwhile, GC contents at the first (GC1s), second (GC2s), third (GC3s) codon positions, mean of GC1s and GC2s (GC12s) and the frequencies of mononucleotides (A, C, U, and G) were calculated using R Language (version 4.0.4).…”

Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases

“…3 ). Uracil rich (U-rich) coding sequences were found in the two open reading frames (ORFs) of broad bean wilt virus 2 (BBWV-2) [60] , the cysteine-rich nucleic acid binding protein (NABP) gene of potato virus M (PVM) [63] , P8 protein coding sequences of RBSDV [61] , coat protein (CP) of CTV [54] , cowpea mild mottle virus (CpMMV) [127] and banana bract mosaic virus (BBrMV) [129] ( Fig. 3 C).…”

“…3 F). For viruses, the AU- or GC-rich composition tends to correlate with their RSCU patterns [60] , [61] , [62] , [63] , [67] , [68] , [132] . For example, an AU-rich composition of SCMV genomes contains codons that frequently end with A and U [62] .…”

“…Gaunt and Digard (2021) reviewed the compositional biases mainly in RNA viruses in terms of the causes, consequences and applications [28] . For plant RNA viruses, several recent studies have reported nucleotide composition, codon usage bias, dinucleotide bias and host or vector adaptation [32] , [39] , [40] , [54] , [55] , [56] , [57] , [58] , [59] , [60] , [61] , [62] , [63] , [64] , [65] . In this review, we summarize evolution and host adaptation in plant RNA viral genomes by considering the compositional biases, and widely used software packages for compositional bias analyses.…”