title: Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes.
abstract: With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes.
authors.affiliation: ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, India.
authors.forename: Ratna
authors.initials: R
authors.lastname: Prabha
authors.affiliation: ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, India. Electronic address: dpsfarm@rediffmail.com.
authors.forename: Dhananjaya P
authors.initials: DP
authors.lastname: Singh
authors.affiliation: Centre for Computational Biology and Bioinformatics, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore City 138671, Singapore.
authors.forename: Swati
authors.initials: S
authors.lastname: Sinha
authors.affiliation: ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, India.
authors.forename: Khurshid
authors.initials: K
authors.lastname: Ahmad
authors.affiliation: ICAR-Indian Agricultural Statistical Research Institute, Indian Council of Agricultural Research, Pusa, New Delhi 110012, India.
authors.forename: Anil
authors.initials: A
authors.lastname: Rai
mesh_terms: D003062:Codon; D000458:Cyanobacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D017422:Sequence Analysis, DNA
chemical_list: D003062:Codon; D004269:DNA, Bacterial
keywords: Codon bias; Codon context; Codon selection pattern; Cyanobacteria; GC composition bias