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- Title
Synonymous Codon Usage Analysis of Three Narcissus Potyviruses.
- Authors
He, Zhen; Ding, Shiwen; Guo, Jiyuan; Qin, Lang; Xu, Xiaowei
- Abstract
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.
- Subjects
POTYVIRUSES; NATURAL selection; PHYTOPLASMAS; GENETIC variation; GENETIC code
- Publication
Viruses (1999-4915), 2022, Vol 14, Issue 5, p846
- ISSN
1999-4915
- Publication type
Article
- DOI
10.3390/v14050846