Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

He, Zhen; Ding, Shiwen; Guo, Jun; Qin, Lang; Xu, Xiaowei

doi:10.3390/v14050846

Cited by 8 publications

(6 citation statements)

References 57 publications

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“…Codon usage patterns of viruses reflect evolutionary changes, such as adaption, evolution, evasion from host immune systems, and survival [ 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. Now, only limited reports show the codon usage patterns of plant viruses, such as citrus tristeza virus (CTV) [ 50 ], rice strape virus (RSV) [ 51 ], papaya ringspot virus (PRSV) [ 52 ], potato virus M (PVM) [ 53 ], sugarcane mosaic virus (SCMV) [ 54 ], broad bean wilt virus 2 (BBWV2) [ 55 ], rice black-streaked dwarf virus (RBSDV) [ 56 ], narcissus degeneration virus (NDV) [ 57 ], narcissus late season yellows virus (NLSYV) [ 57 ], and narcissus yellow stripe virus (NYSV) [ 57 ]. Here, the composition and codon usage patterns of TuMV based on the complete genome were estimated.…”

Section: Discussionmentioning

confidence: 99%

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Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Qin

Ding

Wang

et al. 2022

Viruses

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Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.

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Section: Discussionmentioning

confidence: 99%

“…Low codon usage biases were also observed for RSV, CTV, PRSV, PVM, SCMV, BBWV2, RBSDV, NDV, NLSYV, and NYSV [ 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 ]. For TuMV, similar lower codon usage patterns were also found with ENC values higher than 35, which indicated a low degree of preference.…”

Section: Discussionmentioning

confidence: 99%

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Qin

Ding

Wang

et al. 2022

Viruses

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“…Narcissus yellow stripe virus (NYSV) and Narcissus degeneration virus (NDV) CP genes, a recurring preference for A/U in the third codon position across narcissus viruses was observed (He et al, 2022). This comparative analysis sheds light on the shared characteristics and distinctive features of codon usage among different viruses, providing valuable insights into the evolutionary mechanisms and selective pressures governing codon bias in viral genomes.…”

Section: Comparing Our Ndings With Those Of He Et Al (2022) Who Inves...mentioning

confidence: 86%

Decoding the Genetic Tapestry of Tomato Brown Rugose Fruit Virus: Exploring Evolutionary Adaptation and Codon Usage Bias

Ghorbani

2024

Preprint

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Tomato brown rugose fruit virus (ToBRFV) poses a significant threat to tomato production worldwide, prompting extensive research into its genetic diversity, evolutionary dynamics, and adaptive strategies. In this study, we conducted a comprehensive analysis of ToBRFV at the codon level, focusing on codon usage bias, selection pressures, and evolutionary patterns across multiple genes. Our analysis revealed distinct patterns of codon usage bias and selection pressures within the ToBRFV genome, with varying levels of genetic diversity and evolutionary constraints among different genes. We observed a transition/transversion bias of 2.07 across the entire ToBRFV genome, with the movement protein (MP) gene exhibiting the highest transition/transversion bias and SNP density, suggesting potential evolutionary pressures or a higher mutation rate in this gene. Furthermore, our study identified episodic positive selection primarily in the MP gene, highlighting specific codons subject to adaptive changes in response to host immune pressures or environmental factors. Comparative analysis of codon usage bias in the coat protein (CP) and RNA-dependent RNA polymerase (RdRp) genes revealed gene-specific patterns reflecting functional constraints and adaptation to the host's translational machinery. Our findings provide valuable insights into the molecular mechanisms driving ToBRFV evolution and adaptation, with implications for understanding viral pathogenesis, host-virus interactions, and the development of control strategies. Future research directions include further elucidating the functional significance of codon usage biases, exploring the role of episodic positive selection in viral adaptation, and leveraging these insights to inform the development of effective antiviral strategies and crop protection measures.

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“…Previous studies on plant virus codons such as sugarcane mosaic virus (SCMV) [ 61 ], papaya ringspot virus (PRSV) [ 62 ], potato virus M (PVM) [ 63 ], citrus tristeza virus (CTV) [ 64 ], broad bean wilt virus 2 (BBWV2) [ 65 ], rice stripe virus (RSV) [ 66 ], rice black-streaked dwarf virus (RBSDV) [ 67 ], yellows virus (NLSYV) (NDV) [ 68 ], narcissus degeneration virus narcissus late season [ 68 ] and narcissus yellow stripe virus (NYSV) [ 68 ] have shown that the codon preference of the virus is weak, which is consistent with our analysis results. This phenomenon may be connected to the effective replication of the virus.…”

Section: Discussionmentioning

confidence: 99%

An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus

Wang,

Zhao,

Wang

et al. 2023

Genes

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Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.

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Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Cited by 8 publications

References 57 publications

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Decoding the Genetic Tapestry of Tomato Brown Rugose Fruit Virus: Exploring Evolutionary Adaptation and Codon Usage Bias

An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus

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