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Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

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 t...

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Autores principales: He, Zhen, Ding, Shiwen, Guo, Jiyuan, Qin, Lang, Xu, Xiaowei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9143068/
https://www.ncbi.nlm.nih.gov/pubmed/35632588
http://dx.doi.org/10.3390/v14050846
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author He, Zhen
Ding, Shiwen
Guo, Jiyuan
Qin, Lang
Xu, Xiaowei
author_facet He, Zhen
Ding, Shiwen
Guo, Jiyuan
Qin, Lang
Xu, Xiaowei
author_sort He, Zhen
collection PubMed
description 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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spelling pubmed-91430682022-05-29 Synonymous Codon Usage Analysis of Three Narcissus Potyviruses He, Zhen Ding, Shiwen Guo, Jiyuan Qin, Lang Xu, Xiaowei Viruses Article 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. MDPI 2022-04-19 /pmc/articles/PMC9143068/ /pubmed/35632588 http://dx.doi.org/10.3390/v14050846 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
He, Zhen
Ding, Shiwen
Guo, Jiyuan
Qin, Lang
Xu, Xiaowei
Synonymous Codon Usage Analysis of Three Narcissus Potyviruses
title Synonymous Codon Usage Analysis of Three Narcissus Potyviruses
title_full Synonymous Codon Usage Analysis of Three Narcissus Potyviruses
title_fullStr Synonymous Codon Usage Analysis of Three Narcissus Potyviruses
title_full_unstemmed Synonymous Codon Usage Analysis of Three Narcissus Potyviruses
title_short Synonymous Codon Usage Analysis of Three Narcissus Potyviruses
title_sort synonymous codon usage analysis of three narcissus potyviruses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9143068/
https://www.ncbi.nlm.nih.gov/pubmed/35632588
http://dx.doi.org/10.3390/v14050846
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