Comprehensive codon usage analysis of rice black-streaked dwarf virus based on P8 and P10 protein coding sequences

He, Zhen; Dong, Zhuozhuo; Gan, Haifeng

doi:10.1016/j.meegid.2020.104601

Cited by 9 publications

(18 citation statements)

References 64 publications

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“…Normally, RNA viruses have low codon usage bias to perform efficient replication in the host by lowering the competition with the host genes [55,[65][66][67][68]. Previous reports showed low codon usage bias from several plant viruses such as CTV, PRSV, PVM, RSV and SCMV [19][20][21][22][23][24]. In our study, a lower codon usage pattern of the BBWV2 genome (the ENC values higher than 35) was also found, indicating a low degree of preference.…”

Section: Discussionsupporting

confidence: 67%

“…CUB in viruses is expected to affect their survival, fitness, evolution, adaption, and avoidance of host cell responses [7,13]. Until now, only several reports have described the influence of codon usage in the evolution of plant viruses, such as begomoviruses [18], citrus tristeza virus (CTV) [19], rice black-streaked dwarf virus (RBSDV) [20], rice strape virus (RSV) [21], papaya ringspot virus (PRSV) [22], potato virus M (PVM) [23], and sugarcane mosaic virus (SCMV) [24].…”

Section: Introductionmentioning

confidence: 99%

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

Dong

Qin

et al. 2021

Viruses

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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.

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Section: Discussionsupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

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

Dong

Qin

et al. 2021

Viruses

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“…Natural selection is the main factor density affecting the codon usage bias. Some studies also found that natural selection played an important role in codon usage preferences of the potato virus X (PVX), rice stripe virus (RSV) and rice black-streaked dwarf virus (RBSDV) [ 55 , 56 , 57 ].…”

Section: Discussionmentioning

confidence: 99%

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Ding

Guo³

et al. 2022

Viruses

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Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.

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“…3 A). For single plant virus species, A-rich composition has also been found in all or partial coding region sequences of potato virus Y (PVY) [40] , citrus tristeza virus (CTV) [64] , sugarcane mosaic virus (SCMV) [62] , rice black streak dwarf virus (RBSDV) [61] , narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV) [128] ( Fig. 3 ).…”

Section: Nucleotide Composition Of Plant Rna Virusesmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive codon usage analysis of rice black-streaked dwarf virus based on P8 and P10 protein coding sequences

Cited by 9 publications

References 64 publications

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

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

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

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

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