Arella D, Dilucca M and Giansanti A 2021 Codon usage bias and environmental adaptation in microbial organisms. Mol. Genet. Genom. 296 751–762

CAS  Article  Google Scholar 

Bervoets I and Charlier D 2019 Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol. Rev. 43 304–339

CAS  PubMed  PubMed Central  Article  Google Scholar 

Brandis G and Hughes D 2016 The selective advantage of synonymous codon usage bias in Salmonella. PLoS Genet. 12 e1005926

PubMed  PubMed Central  Article  CAS  Google Scholar 

Butt AM, Nasrullah I, Qamar R and Tong Y 2016 Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg. Microbes Infect. 5 e107

CAS  PubMed  PubMed Central  Article  Google Scholar 

Butt AM, Nasrullah I and Tong Y 2014 Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PLoS One 9 e90905

PubMed  PubMed Central  Article  CAS  Google Scholar 

Carbone A, Kepes F and Zinovyev A 2005 Codon bias signatures, organization of microorganisms in codon space, and lifestyle. Mol. Biol. Evol. 22 547–561

CAS  PubMed  Article  Google Scholar 

Chen L, Liu T, Yang D, et al. 2013 Analysis of codon usage patterns in Taenia pisiformis through annotated transcriptome data. Biochem. Biophys. Res. Commun. 430 1344–1348

CAS  PubMed  Article  Google Scholar 

Dilucca M, Pavlopoulou A, Georgakilas AG and Giansanti A 2020 Codon usage bias in radioresistant bacteria. Gene 742 144554

CAS  PubMed  Article  Google Scholar 

Feil H, Feil WS, Chain P, et al. 2005 Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 102 11064–11069

CAS  PubMed  PubMed Central  Article  Google Scholar 

Frank A and Lobry J 1999 Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238 65–77

CAS  PubMed  Article  Google Scholar 

Gouy M and Gautier C 1982 Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10 7055–7074

CAS  PubMed  PubMed Central  Article  Google Scholar 

He B, Dong H, Jiang C, et al. 2016 Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending. Sci. Rep. 6 35927

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hershberg R and Petrov DA 2009 General rules for optimal codon choice. PLoS Genet. 5 e1000556

PubMed  PubMed Central  Article  CAS  Google Scholar 

Ikemura T 1981 Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151 389–409

CAS  PubMed  Article  Google Scholar 

James FC and McCulloch CE 1990 Multivariate analysis in ecology and systematics: panacea or Pandora’s box? Annu. Rev. Ecol. Syst. 21 129–166

Article  Google Scholar 

Jenkins GM and Holmes EC 2003 The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92 1–7

CAS  PubMed  Article  Google Scholar 

Khandia R, Singhal S, Kumar U, et al. 2019 Analysis of Nipah virus codon usage and adaptation to hosts. Front. in Microbiol. 10 886

Article  Google Scholar 

Kiil K, Binnewies TT, Willenbrock H, et al. 2008 Comparative genomics of Pseudomonas; in Pseudomonas: Model organism, pathogen, cell factory (Wiley) pp 1–24

LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT and abd Rokas A 2019 Variation and selection on codon usage bias across an entire subphylum. PLoS Genet. 15 e1008304

PubMed  PubMed Central  Article  CAS  Google Scholar 

Li J, Zhou J, Wu Y, Yang S and Tian D 2015 GC-content of synonymous codons profoundly influences amino acid usage. G3 5 2027–2036

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mondal SK, Kundu S, Das R and Roy S 2016 Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes. J. Biomol. Struct. Dyn. 34 1649–1666

CAS  PubMed  Article  Google Scholar 

Mueller S, Papamichail D, Coleman JR, Skiena S and Wimmer E 2006 Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J. Virol. 80 9687–9696

CAS  PubMed  PubMed Central  Article  Google Scholar 

Musto H, Romero H and Zavala A 2003 Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum. Microbiology 149 855–863

CAS  PubMed  Article  Google Scholar 

Nie X, Deng P, Feng K, et al. 2014 Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family. Plant Mol. Biol. Rep. 32 828–840

CAS  Article  Google Scholar 

Post LE and Nomura M 1980 DNA sequences from the str operon of Escherichia coli. J. Biol. Chem. 255 4660–4666

CAS  PubMed  Article  Google Scholar 

Sau K, Gupta SK, Sau S, Mandal SC and Ghosh TC 2006 Factors influencing synonymous codon and amino acid usage biases in Mimivirus. Biosystems 85 107–113

CAS  PubMed  Article  Google Scholar 

Sharp PM, Bailes E, Grocock RJ, Peden JF and abd Sockett RE, 2005 Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33 1141–1153

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sharp PM and Li W-H 1986 Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’codons. Nucleic Acids Res. 14 7737–7749

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sharp PM and Li W-H 1987 The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 1281–1295

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sharp PM, Stenico M, Peden JF and abd Lloyd AT 1993 Codon usage: mutational bias, translational selection, or both? Biochem. Soc. Trans. 21 835–841

CAS  PubMed  Article  Google Scholar 

Simón D, Cristina J and Musto H 2021 Nucleotide composition and codon usage across viruses and their respective hosts. Front. Microbiol. 12 646300

PubMed  PubMed Central  Article  Google Scholar 

Šmarda P, Bureš P, Horová L, et al. 2014 Ecological and evolutionary significance of genomic GC content diversity in monocots. Proc. Natl. Acad. Sci. USA 111 E4096–E4102

PubMed  PubMed Central  Article  CAS  Google Scholar 

Sueoka N 1988 Directional mutational pressure and neutral pressure. Proc. Natl. Acad. Sci. USA 85 2653–2657

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sueoka N 1995 Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J. Mol. Evol. 40 318–325

CAS  PubMed  Article  Google Scholar 

Sueoka N 1999 Two aspects of DNA base composition: G+ C content and translation-coupled deviation from intra-strand rule of A=T and G=C. J. Mol. Evol. 49 49–62

CAS  PubMed  Article  Google Scholar 

Sueoka N and Kawanishi Y 2000 DNA G+ C content of the third codon position and codon usage biases of human genes. Gene 261 53–62

CAS  PubMed  Article  Google Scholar 

Tanaka T, Koyanagi KO and Itoh T 2009 Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis. Plant Physiol. 149 1316–1324

CAS  PubMed  PubMed Central  Article  Google Scholar 

Vicario S, Moriyama EN and Powell JR 2007 Codon usage in twelve species of Drosophila. BMC Evol. Biol. 7 226

PubMed  PubMed Central  Article  CAS  Google Scholar 

Wang H-C and Hickey DA 2007 Rapid divergence of codon usage patterns within the rice genome. BMC Evol. Biol. 7 https://doi.org/10.1186/1471-2148-7-S1-S6