Codon usage bias of the phosphoprotein gene of spring viraemia of carp virus and high codon adaptation to the host

Ma, Yuanfang; Zhou, Zhiwei; Liu, Zhenxing; Liang, Hao; Ma, Jin-Yeul; Feng, Guoqing; Liang, Zhiling; Hao, Ke

doi:10.1007/s00705-014-2000-z

Cited by 6 publications

(3 citation statements)

References 42 publications

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“…These results suggest that the selection pressure from the hosts may influence the codon usage pattern of ZIKV, which may assist it in adapting to the cellular environment of the hosts and allow it to replicate efficiently in the hosts [24, 31]. Interestingly, the role of the translational selection from H .…”

Section: Resultsmentioning

confidence: 99%

“…Analysis of the correlation between the GC contents at the first and second codon positions (GC12) and that at the third codon position (GC3) is useful to examine the effect of mutation pressure and translational selection on the base composition [31]. Therefore, GC12 and GC3 were calculated by using the EMBOSS CUSP program [32] and then subjected to correlation analysis.…”

Section: Methodsmentioning

confidence: 99%

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Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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“…Studies have shown that the higher the gene expression level is, the stronger is the preferred use of codon [1][2][3]6,15,16,49,[55][56][57][58][59][60]. In our study, the codon usage bias results of all cotton species were shown in S1 Table. The correlation between the parameters of 4 cotton species and 4 subgenomes had the same rule, except the correlation between G3s and C3s.…”

Section: Correlation Analysis Between Codon Usage Bias Indicesmentioning

confidence: 74%

Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

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Comparative analysis of codon usage patterns of venom gland-specific honeybee-infecting viruses in solitary hunting and social wasps

Andrew Yoon,

Jin Kim,

Hyeock Lee

2024

Journal of Asia-Pacific Entomology

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Codon usage bias of the phosphoprotein gene of spring viraemia of carp virus and high codon adaptation to the host

Cited by 6 publications

References 42 publications

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Genome-wide analysis of codon usage bias in four sequenced cotton species

Comparative analysis of codon usage patterns of venom gland-specific honeybee-infecting viruses in solitary hunting and social wasps

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