Codon Usage Bias: An Endless Tale

Iriarte, Andrés; Lamolle, Guillermo; Musto, Héctor

doi:10.1007/s00239-021-10027-z

Cited by 65 publications

(37 citation statements)

References 41 publications

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“…The frequency of codon usage is not usually random, and it has been linked to translation efficiency, mutational drift, and other selection pressures such as natural selection ( Bulmer, 1991 ; Hershberg & Petrov, 2009 ; Iriarte, Lamolle & Musto, 2021 ; Komar, 2016 ; Musto, 2016 ; Novoa et al, 2019 ; Sharp, Emery & Zeng, 2010 ; Supek, 2016 ). Among them, mutational pressure and natural selection are the two driving forces shaping the codon usage bias of a gene.…”

Section: Discussionmentioning

confidence: 99%

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)

Tyagi

Sardar

Gupta

2022

PeerJ

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The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC.

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Section: Discussionmentioning

confidence: 99%

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)

Tyagi

Sardar

Gupta

2022

PeerJ

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“…Biological beings share a set of 20 amino acids, eighteen of which can be encoded by more than one synonymous codon. The codon usage frequency is usually not random, and has been related to translation efficiency and accuracy, mutational drift, and other selection pressures ( Bulmer, 1991 ; Hershberg and Petrov, 2009 ; Iriarte et al, 2021 ; Komar, 2016 ; Musto, 2016 ; Novoa et al, 2019 ; Sharp et al, 2010 ; Supek, 2016 ). In general, viruses only show a slight codon usage bias (CUB), mainly explained by uneven base composition and, hence, by mutation pressure ( Shackelton et al, 2006 ).…”

Section: Introductionmentioning

confidence: 99%

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

2022

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SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.

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“…In addition, codon usage bias (CUB), referring to the unbalanced utilization of synonymous codons in coding DNA, can be analyzed for getting insights into the evolutionary patterns of both taxa and genes [ 34 , 35 , 36 , 37 , 38 ]. By the statistical analysis of CUB, we can speculate which factor is mainly responsible for bias pattern, usually mutational bias or natural selection [ 39 , 40 , 41 ].…”

Section: Introductionmentioning

confidence: 99%

Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

Han¹,

Wang

Hong

et al. 2022

IJMS

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The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.

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Codon Usage Bias: An Endless Tale

Cited by 65 publications

References 41 publications

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

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