Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Qin, Lang; Ding, Shiwen; Wang, Zhilei; Jiang, Runzhou; He, Zhen

doi:10.3390/v14102267

Cited by 11 publications

(8 citation statements)

References 59 publications

(106 reference statements)

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“…Moreover, our study contributes to understanding the mutation pressures shaping codon usage in ToBRFV genes. We found a preference for A/G in TuMV protein-coding regions, indicative of mutation pressures (Qin et al, 2022). This insight underscores the dynamic nature of codon usage and its implications for viral evolution and adaptation.…”

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

confidence: 52%

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

confidence: 52%

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

Ghorbani

2024

Preprint

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“…The results of this index were in line with the CAI index. A low RCDI may suggest a strong adaptation to the host [47, 48], while in the CAI index, this phenomenon is vice versa.…”

Section: Resultsmentioning

confidence: 99%

“…The results of this index were in line with the CAI index. A low RCDI may suggest a strong adaptation to the host [47,48], while in the CAI index, this phenomenon is vice versa. The field of plant virus phylogenetics has advanced significantly due to the exponential increase in available genome sequence data and the development of dedicated bioinformatics tools for analyzing these data.…”

Section: The Rcdi Analysismentioning

confidence: 99%

Investigation of CaMV‐host co‐evolution through synonymous codon pattern

Pouresmaeil,

Azizi‐Dargahlou

2024

J Basic Microbiol

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Cauliflower mosaic virus (CaMV) has a double‐stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co‐evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)‐plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.

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“…A slope approaching 1 suggests that codon usage is primarily influenced by mutation pressure. Conversely, a slope closer to zero signifies that natural selection plays a more prominent role in shaping the bias of codon usage [34].…”

Section: Methodsmentioning

confidence: 99%

Codon usage bias of human papillomavirus type 33 and 58: A comprehensive analysis

Tan,

Xie,

Jiang

et al. 2024

J Basic Microbiol

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Cervical cancer is closely linked to specific strains of human papillomavirus (HPV), notably HPV‐33 and HPV‐58, which exhibit a significant prevalence among women in China. Nevertheless, the codon usage bias in HPV‐33 and HPV‐58 is not well comprehended. The objective of this research is to analyze the codon usage patterns HPV‐33 and HPV‐58, pinpoint the primary factors that influence codon preference. The overall preference for codon usage in two HPV genotypes is not significant. Both HPV genotypes exhibit a preference for codons that end with A/U. The GC3 content for HPV‐33 is 25.43% ± 0.35%, and for HPV‐58, it is 29.44% ± 0.57%. Out of the 26 favored codons in HPV‐33 and HPV‐58 (relative synonymous codon usage (RSCU) > 1), 25 conclude with A/U. Principal component analysis (PCA) shows a tight clustering of the entire genome sequences of HPV‐33 and HPV‐58, suggesting a similarity in their RSCU preferences. Moreover, an examination of dinucleotide abundance indicated that translation selection influenced the development of a distinctive dinucleotide usage pattern in HPV‐33 and HPV‐58. Additionally, a combined analysis involving an effective number of codons plot, parity rule 2, and neutrality analysis demonstrated that, for HPV‐33 and HPV‐58, the primary determinant influencing codon usage preference is natural selection. HPV‐33 and HPV‐58 exhibit a restricted set of favored codons in common with humans, potentially mitigating competition for translation resources. Our discoveries could provide valuable perspectives on the evolutionary patterns and codon usage preferences of HPV‐33 and HPV‐58 viruses, contributing to the development and application of relevant HPV subtype vaccines.

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Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Cited by 11 publications

References 59 publications

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

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

Investigation of CaMV‐host co‐evolution through synonymous codon pattern

Codon usage bias of human papillomavirus type 33 and 58: A comprehensive analysis

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