An interplay between compositional constraint and natural selection dictates the codon usage pattern among select Galliformes

AbstractSynonymous codons are used with different frequencies, a phenomenon known as codon bias, which exists in many genomes and is mainly resolute by mutation and selection. To elucidate the genetic characteristics and evolutionary relationship ofWucheraria bancroftiandSchistosoma haematobiumwe examined the pattern of synonymous codon usage in nuclear genes of both the species. The mean overall GC contents ofW. bancroftiandS. haematobiumwere 43.41 and 36.37%, respectively, which suggests that genes in both the species were AT rich. The value of the High Effective Number of Codons in both species suggests that codon usage bias was weak. Both species had a wide range of P3 distribution in the neutrality plot, with a significant correlation between P12 and P3. The codons were closer to the axes in correspondence analysis, suggesting that mutation pressure influenced the codon usage pattern in these species. We have identified the more frequently used codons in these species, most codons ending with an A or T. The nucleotides A/T and C/G were not proportionally used at the third position of codons, which reveals that natural selection might influence the codon usage patterns. The regression equation of P12 on P3 suggests that natural selection might have played a major role, while mutational pressure played a minor role in codon usage pattern in both species. These results form the basis of exploring the evolutionary mechanisms and the heterologous expression of medically important proteins ofW. bancroftiandS. haematobium.

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Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Viruses ◽

10.3390/v11080752 ◽

2019 ◽

Vol 11 (8) ◽

pp. 752 ◽

Cited By ~ 8

Author(s):

Zhen He ◽

Haifeng Gan ◽

Xinyan Liang

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Potato Virus ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Economic Losses ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Coding Sequences ◽

Potato Virus M

Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.

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Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

BioMed Research International ◽

10.1155/2019/5857285 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 3

Author(s):

Huipeng Yao ◽

Mengyu Chen ◽

Zizhong Tang

Keyword(s):

Phylogenetic Analysis ◽

Natural Selection ◽

Correlation Analysis ◽

Codon Usage ◽

Codon Usage Bias ◽

Yellow Fever Virus ◽

Gc Content ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Group I

Background. Flaviviridae viruses are single-stranded, positive-sense RNA viruses, which threat human constantly mediated by mosquitoes, ticks, and sandflies. Considering the recent increase in the prevalence of the family virus and its risk potential, we investigated the codon usage pattern to understand its evolutionary processes and provide some useful data to develop the medications for most of Flaviviridae viruses. Results. The overall extent of codon usage bias in 65 Flaviviridae viruses is low with the average value of GC contents being 50.5% and the highest value being 55.9%; the lowest value is 40.2%. ENC values of Flaviviridae virus genes vary from 48.75 to 57.83 with a mean value of 55.56. U- and A-ended codons are preferred in the Flaviviridae virus. Correlation analysis shows that the positive correlation between ENC value and GC content at the third nucleotide positions was significant in this family virus. The result of analysis of ENC, neutrality plot analysis, and correlation analysis revealed that codon usage bias of all the viruses was affected mainly by natural selection. Meanwhile, according to correspondence analysis (CoA) based on RSCU and phylogenetic analysis, the Flaviviridae viruses mainly are made up of two groups, Group I (Yellow fever virus, Apoi virus, Tembusu virus, Dengue virus 1, and others) and Group II (West Nile virus lineage 2, Japanese encephalitis virus, Usutu virus, Kedougou virus, and others). Conclusions. All in, the bias of codon usage pattern is affected not only by compositional constraints but also by natural selection. Phylogenetic analysis also illustrates that codon usage bias of virus can serve as an effective means of evolutionary classification in Flaviviridae virus.

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Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus

International Journal of Molecular Sciences ◽

10.3390/ijms21197129 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7129

Author(s):

Jiumeng Sun ◽

Wen Zhao ◽

Ruyi Wang ◽

Wenyan Zhang ◽

Gairu Li ◽

...

Keyword(s):

Influenza Virus ◽

Natural Selection ◽

Codon Usage ◽

Selection Pressure ◽

Gallus Gallus ◽

Codon Usage Pattern ◽

Usage Pattern ◽

H7n9 Influenza Virus ◽

Evolutionary Changes ◽

H7n9 Influenza

Novel H7N9 influenza virus transmitted from birds to human and, since March 2013, it has caused five epidemic waves in China. Although the evolution of H7N9 viruses has been investigated, the evolutionary changes associated with codon usage are still unclear. Herein, the codon usage pattern of two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), was studied to understand the evolutionary changes in relation to host, epidemic wave, and pathogenicity. Both genes displayed a low codon usage bias, with HA higher than NA. The codon usage was driven by mutation pressure and natural selection, although the main contributing factor was natural selection. Additionally, the codon adaptation index (CAI) and deoptimization (RCDI) illustrated the strong adaptability of H7N9 to Gallus gallus. Similarity index (SiD) analysis showed that Homo sapiens posed a stronger selection pressure than Gallus gallus. Thus, we assume that this may be related to the gradual adaptability of the virus to human. In addition, the host strong selection pressure was validated based on CpG dinucleotide content. In conclusion, this study analyzed the usage of codons of two genes of H7N9 and expanded our understanding of H7N9 host specificity. This aids into the development of control measures against H7N9 influenza virus.

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Prediction of gene expression under drought stress in spring wheat using codon usage pattern

Saudi Journal of Biological Sciences ◽

10.1016/j.sjbs.2021.04.015 ◽

2021 ◽

Author(s):

Meshal M. Almutairi ◽

Abdullah A. Alrajhi

Keyword(s):

Gene Expression ◽

Drought Stress ◽

Codon Usage ◽

Spring Wheat ◽

Codon Usage Pattern ◽

Usage Pattern

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Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae

Archives of Virology ◽

10.1007/s00705-020-04890-2 ◽

2021 ◽

Author(s):

Bornali Deb ◽

Arif Uddin ◽

Supriyo Chakraborty

Keyword(s):

Codon Usage ◽

Influencing Factors ◽

Codon Usage Pattern ◽

Usage Pattern ◽

The Family ◽

Protein Properties

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Analysis of codon usage bias of classical swine fever virus

Veterinary World ◽

10.14202/vetworld.2021.1450-1458 ◽

2021 ◽

pp. 1450-1458

Author(s):

Sharanagouda S. Patil ◽

Uma Bharathi Indrabalan ◽

Kuralayanapalya Puttahonnappa Suresh ◽

Bibek Ranjan Shome

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Principal Component ◽

Infectious Agent ◽

Classical Swine Fever ◽

Economic Loss ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Coding Regions

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

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