Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2
Broad bean wilt virus 2 (BBWV-2), which belongs to the genus <i>Fabavirus</i> of the family <i>Secoviridae</i>, is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previ...
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MDPI AG
2021-01-01
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| Online Access: | https://www.mdpi.com/1999-4915/13/2/198 |
| _version_ | 1827597023850790912 |
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| author | Zhen He Zhuozhuo Dong Lang Qin Haifeng Gan |
| author_facet | Zhen He Zhuozhuo Dong Lang Qin Haifeng Gan |
| author_sort | Zhen He |
| collection | DOAJ |
| description | Broad bean wilt virus 2 (BBWV-2), which belongs to the genus <i>Fabavirus</i> of the family <i>Secoviridae</i>, 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<sup>−4</sup> and 4.560 × 10<sup>−4</sup> 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. |
| first_indexed | 2024-03-09T03:22:26Z |
| format | Article |
| id | doaj.art-5d6eb1b3fb914dd28101a3644a9b4e18 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T03:22:26Z |
| publishDate | 2021-01-01 |
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| series | Viruses |
| spelling | doaj.art-5d6eb1b3fb914dd28101a3644a9b4e182023-12-03T15:06:14ZengMDPI AGViruses1999-49152021-01-0113219810.3390/v13020198Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2Zhen He0Zhuozhuo Dong1Lang Qin2Haifeng Gan3School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, ChinaSchool of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, ChinaSchool of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, ChinaSchool of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, ChinaBroad bean wilt virus 2 (BBWV-2), which belongs to the genus <i>Fabavirus</i> of the family <i>Secoviridae</i>, 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<sup>−4</sup> and 4.560 × 10<sup>−4</sup> 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.https://www.mdpi.com/1999-4915/13/2/198broad bean wilt virus 2codon usage patternnatural selectionhost adaptation |
| spellingShingle | Zhen He Zhuozhuo Dong Lang Qin Haifeng Gan Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2 Viruses broad bean wilt virus 2 codon usage pattern natural selection host adaptation |
| title | Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2 |
| title_full | Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2 |
| title_fullStr | Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2 |
| title_full_unstemmed | Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2 |
| title_short | Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2 |
| title_sort | phylodynamics and codon usage pattern analysis of broad bean wilt virus 2 |
| topic | broad bean wilt virus 2 codon usage pattern natural selection host adaptation |
| url | https://www.mdpi.com/1999-4915/13/2/198 |
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