Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

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Analysis of synonymous codon usage patterns in different plant mitochondrial genomes

Molecular Biology Reports ◽

10.1007/s11033-008-9414-1 ◽

2008 ◽

Vol 36 (8) ◽

pp. 2039-2046 ◽

Cited By ~ 33

Author(s):

Meng Zhou ◽

Xia Li

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Mitochondrial Genomes ◽

Usage Patterns

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Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China

Research in Veterinary Science ◽

10.1016/j.rvsc.2019.09.012 ◽

2019 ◽

Vol 127 ◽

pp. 42-46 ◽

Cited By ~ 3

Author(s):

Xin Xu ◽

Pengfei Li ◽

Yating Zhang ◽

Xianhe Wang ◽

Jiaxin Xu ◽

...

Keyword(s):

Codon Usage ◽

Porcine Epidemic Diarrhea Virus ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Comprehensive Analysis ◽

Orf3 Gene ◽

Diarrhea Virus ◽

Usage Patterns ◽

Porcine Epidemic Diarrhea

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Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes

Genetics and Molecular Research ◽

10.4238/2013.february.27.8 ◽

2013 ◽

Vol 12 (1) ◽

pp. 587-596 ◽

Cited By ~ 8

Author(s):

L. Chen ◽

D.Y. Yang ◽

T.F. Liu ◽

X. Nong ◽

X. Huang ◽

...

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Mitochondrial Genomes ◽

Usage Patterns ◽

Parasitic Platyhelminth

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Analysis of synonymous codon usage patterns in torque teno sus virus 1 (TTSuV1)

Archives of Virology ◽

10.1007/s00705-012-1480-y ◽

2012 ◽

Vol 158 (1) ◽

pp. 145-154 ◽

Cited By ~ 21

Author(s):

Zhicheng Zhang ◽

Wei Dai ◽

Yang Wang ◽

Chengping Lu ◽

Hongjie Fan

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Usage Patterns ◽

Torque Teno Sus Virus

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Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family

Australian Journal of Botany ◽

10.1071/bt12073 ◽

2012 ◽

Vol 60 (5) ◽

pp. 461 ◽

Cited By ~ 10

Author(s):

Yuerong Zhang ◽

Xiaojun Nie ◽

Xiaoou Jia ◽

Cunzhen Zhao ◽

Siddanagouda S. Biradar ◽

...

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Mutational Bias ◽

Plot Analysis ◽

Optimal Codons ◽

Chloroplast Genomes ◽

Usage Patterns ◽

Poaceae Family ◽

High Representation

Codon usage patterns of 23 Poaceae chloroplast genomes were analysed in this study. Neutrality analysis indicated that the codon usage patterns have significant correlations with GC12 and GC3 and also showed strong bias towards a high representation of NNA and NNT codons. The Nc-plot showed that although a large proportion of points follow the parabolic line of trajectory, several genes with low ENc values lie below the expected curve, suggesting that mutational bias played a major role in the codon biology of the Poaceae chloroplast genome. Parity Rule 2 plot analysis showed that T was used more frequently than A in all the genomes. Correspondence analysis of relative synonymous codon usage indicated that the first axis explained only a partial amount of variation of codon usage. Furthermore, the gene length and expression level were also found to drive codon usage variation. These findings revealed that besides natural selection, other factors might also exert some influences in shaping the codon usage bias in Poaceae chloroplast genomes. The optimal codons of these 23 genomes were also identified in this study.

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Natural Selection Determines Synonymous Codon Usage Patterns of Neuraminidase (NA) Gene of the Different Subtypes of Influenza A Virus in Canada

Journal of Viruses ◽

10.1155/2014/329049 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Youhua Chen

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Influenza A Virus ◽

Influenza A ◽

Synonymous Codon ◽

Phylogenetic Signal ◽

Synonymous Codon Usage ◽

Usage Patterns ◽

Na Sequences ◽

Na Gene

Synonymous codon usage patterns of neuraminidase (NA) gene of 64 subtypes (one is a mixed subtype) of influenza A virus found in Canada were analyzed. In total, 1422 NA sequences were analyzed. Among the subtypes, H1N1 is the prevailing one with 516 NCBI accession records, followed by H3N2, H3N8, and H4N6. The year of 2009 has the highest report records for the NA sequences in Canada, corresponding to the 2009 pandemic event. Correspondence analysis on the RSCU values of the four major subtypes showed that they had distinct clustering patterns in the two-dimensional scatter plot, indicating that different subtypes of IAV utilized different preferential codons. This subtype clustering pattern implied the important influence of natural selection, which could be further evidenced by an extremely flattened regression line in the neutrality plot (GC12 versus G3s plot) and a significant phylogenetic signal on the distribution of different subtypes in the clades of the phylogenetic tree (λ statistic). In conclusion, different subtypes of IAV showed an evolutionary differentiation on choosing different optimal codons. Natural selection played a deterministic role to structure IAV codon usage patterns in Canada.

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