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

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

Biosystems ◽

10.1016/j.biosystems.2021.104390 ◽

2021 ◽

pp. 104390

Author(s):

Indrani Sarkar ◽

Saurabh Singh Rathore ◽

Ram Pratap Singh

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Compositional Constraint

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Expression levels and codon usage patterns in nuclear genes of the filarial nematodeWucheraria bancroftiand the blood flukeSchistosoma haematobium

Journal of Helminthology ◽

10.1017/s0022149x16000092 ◽

2016 ◽

Vol 91 (1) ◽

pp. 72-79 ◽

Cited By ~ 5

Author(s):

G.A. Mazumder ◽

A. Uddin ◽

S. Chakraborty

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Evolutionary Relationship ◽

Nuclear Genes ◽

Codon Usage Pattern ◽

Minor Role ◽

Usage Pattern ◽

Genetic Characteristics ◽

Wide Range ◽

Usage Patterns

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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Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern

Virulence ◽

10.1080/21505594.2018.1551708 ◽

2018 ◽

Vol 10 (1) ◽

pp. 1-9 ◽

Cited By ~ 10

Author(s):

Ziqing Yan ◽

Ruyi Wang ◽

Letian Zhang ◽

Binger Shen ◽

Ningning Wang ◽

...

Keyword(s):

Codon Usage ◽

Fusion Gene ◽

Codon Usage Pattern ◽

The Novel ◽

Usage Pattern ◽

Evolutionary Changes

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Comprehensive analysis of codon usage pattern of whole genome in protozoa, Stylonychia lemnae

10.21203/rs.2.16114/v1 ◽

2019 ◽

Author(s):

Ying Wang ◽

Lin Yao ◽

Jinfeng Fan ◽

Xueying Zhang ◽

Changhong Guo ◽

...

Keyword(s):

Codon Usage ◽

Classical Model ◽

Mrna Translation ◽

Codon Usage Pattern ◽

Translational Efficiency ◽

Usage Pattern ◽

Evolutionary Origins ◽

Plot Analysis ◽

Evolutionary Changes ◽

Usage Patterns

Abstract Background: Codon usage pattern is an important evolutionary feature in genomes widely observed in many organisms. Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a germline micronucleus and a vegetative macronucleus. Analysis of codon usage pattern of S. lemnae macronucleus genome helps in understanding evolution at molecular level and acquires signiﬁcance in mRNA translation, design of transgenic and new gene discovery. Results: The codons of the macronucleus genome sequence of S. lemnae were analyzed and 20,750 coding sequences (CDS) were screened. The overall codon usage of S. lemnae is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in S. lemnae is relatively high. Nucleotide analysis showed that the overall codon usage is biased toward A- and U-ending codons. The phylogenetic analysis indicated that ciliate is independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of S. lemnae is more similar to that of Thtrahymana thermophila and Paramecium caudatum . Correlation analysis, ENC-GC 3S plot, and PR2 plot indicated that the codon usage patterns of S. lemnae are not only influenced by mutational pressure but also by natural selection, but neutrality plot analysis showed that the latter plays a major role. C onclusions : Codon usage patterns in eukaryotes are not determined by translational efficiency, but also are determined by the genome. Our study is the ﬁrst attempt to evaluate the codon usage pattern of S.lemnae macronucleus genome to better understand the evolutionary changes. These results built the base for further research on the molecular evolution of S. lemnae .

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