Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus

Nguyen, Thi Hung; Wang, Dong; Rahman, Siddiq Ur; Bai, Haoxiang; Yao, Xiaoting; Chen, Dekun; Tao, Shiheng

doi:10.1016/j.meegid.2021.104750

Cited by 12 publications

(9 citation statements)

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“…As parasitic organisms, viruses have some characteristics in their genomes different from prokaryotes and eukaryotes, for instance, relying on their hosts' translational machinery for gene expression. This virushost interaction influence the overall viral survival, adaptation, evasion of the host immune response, and evolution (Nasrullah et al, 2015;Rahman et al, 2017;Nguyen et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

et al. 2021

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The molecular evolutionary dynamics that shape hantaviruses’ evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two aspects in Hantaan virus (HTNV)—the prototype of hantaviruses and an emerging zoonotic pathogen that infects humans, causing hemorrhagic fever with renal syndrome (HFRS): endemic in Far East Russia, China, and South Korea—via a comprehensive, phylogenetic-dependent codon usage analysis. We found that host- and natural reservoir-induced natural selection is the primary determinant of its biased codon choices, exceeding the mutational bias effect. The phylogenetic analysis of HTNV strains resulted in three distinct clades: South Korean, Russian, and Chinese. An effective number of codon (ENC) analysis showed a slightly biased codon usage in HTNV genomes. Nucleotide composition and RSCU analyses revealed a significant bias toward A/U nucleotides and A/U-ended codons, indicating the potential influence of mutational bias on the codon usage patterns of HTNV. Via ENC-plot, Parity Rule 2 (PR2), and neutrality plot analyses, we would conclude the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of HTNV; however, natural selection is the dominant factor influencing its codon usage bias. Codon adaptation index (CAI), Relative codon deoptimization index (RCDI), and Similarity Index (SiD) analyses uncovered the intense selection pressure from the host (Human) and natural reservoirs (Striped field mouse and Chinese white-bellied rat) in shaping HTNV biased codon choices. Our study clearly revealed the evolutionary processes in HTNV and the role of virus-host interaction in its evolution. Moreover, it opens the door for a more comprehensive codon usage analysis for all hantaviruses species to determine their molecular evolutionary dynamics and adaptability to several hosts and environments. We believe that our research will help in a better and deep understanding of HTNV evolution that will serve its future basic research and aid live attenuated vaccines design.

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Section: Introductionmentioning

confidence: 99%

Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

et al. 2021

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“…In our study, this CpG deficiency composition in PEDV and perhaps other RNA viruses, has the potential possibility to benefit the viruses to adapt to their host and escape the host’s defense system. Studies have shown that RNA viruses generally have low CUB, and their ENC values are in the range of 47.62–57.23 ( Hu et al, 2011 ; Lara-Ramírez et al, 2014 ; Cristina et al, 2015 ; Zhou et al, 2019 ; Nguyen et al, 2021 ), which would facilitate virus replication and adaptation to the host immune system ( Chen et al, 2014 ; Khandia et al, 2019 ). In order to prove whether the CUB in PEDV genome follows this rule, we calculated the ENC value in each genome and the results in this study indicated that there is a low CUB in all PEDV isolates with the mean ENC value of 48.1 ( Supplementary Table 2 ), this value falls in the low bias range and was compatible with the similar study on PEDV ( Chen et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

“…It is worth to note that COA analysis found that two phylogroups of PEDV clustered separately between the first two axes, indicating that the codon usage pattern between different phylogroups have difference. Apart from those two selection pressures, reports have showed that other factors such as geographic distribution ( Chen et al, 2014 ; Nguyen et al, 2021 ) and relative dinucleotide frequencies ( Cheng et al, 2020 ; Munjal et al, 2020 ) also acts as the driving forces in shaping the codon usage pattern in many RNA viruses. Specifically in our study, unique dinucleotide usage pattern and the relative dinucleotide frequencies show that dinucleotide composition also plays a role in the synonymous codon usage pattern of PEDV.…”

Section: Discussionmentioning

confidence: 99%

“…The phenomenon is called as codon usage bias (CUB). CUB exists in the genomes of all species including viruses, it is regarded as a driving force of genetic evolution ( Deb et al, 2021 ; Huang et al, 2021 ; Nguyen et al, 2021 ) and is suggested to play an important role in the adaptation of various viruses to their host ( Butt et al, 2016 ; Kumar et al, 2018 ; Tian et al, 2018 ; Khandia et al, 2019 ; Luo et al, 2020a ). It is also suggested that codon usage of viruses is not limited to host adaption, but is also critical in various biological processes including viral gene transcription, nuclear export of virus RNA, tolerance to translation errors and immune escape ( Zhou et al, 2016 ; Kumar et al, 2021 ; Mordstein et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype

Jiang

et al. 2021

Front. Microbiol.

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Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.

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“…Codon usage bias influences transcription [12,13], protein translation [14,15] and gene expression levels [16,17]. Thus, the codon usage bias pattern provides important information for reconstruction vectors and for the improvement of expression levels, as well as for the revelation of plant-pathogen coevolutionary events and the improvement of host resistance [18][19][20]. Previous research has found that codon usage, frequently of highand low-GC-content genes, is different in B. distachyon Bd21, and 27 codons were identified as optimal for evolution studies [8].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5′-ends to the 3′-ends

Jian-Yong

Lin

Mao

2021

Genes

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Brachypodium distachyon, a new monocotyledonous model plant, has received wide attention in biological research due to its small genome and numerous genetic resources. Codon usage bias is an important feature of genes and genomes, and it can be used in transgenic and evolutionary studies. In this study, the nucleotide compositions and patterns of codon usage bias were calculated using Codon W. Additionally, an ENC plot, Parity rule 2 and correspondence analyses were used to explore the major factors influencing codon usage bias patterns. The numbers of hydrogen bonds and skews were used to analyze the GC trend in the 5′-ends of the coding sequences. The results showed that minor differences in the codon usage bias patterns were revealed by the ENC plot, Parity rule 2 and correspondence analyses. The analyses of the CG-skew and the number of hydrogen bonds showed a declining trend in the number of cytosines at the 5′-ends of the CDSs (from the 5′-ends to the 3′-ends), indicating that GC may play a major role in codon usage bias. In addition, our results laid a foundation for the study of codon usage bias patterns in Brachypodium genus and suggested that the GC plays a major role in determining these patterns.

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Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus

Cited by 12 publications

References 58 publications

Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype

Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5′-ends to the 3′-ends

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