title: Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective.
abstract: Genome analysis of thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 revealed factors ruling choices of codons in this organism. Multiple parameters like Nc, GC3s, RSCU, Codon Adaptation Index (CAI), optimal and rare codons, codon-pair context and amino acid usage were analysed and compositional constraint was identified as major factor. Wide range of Nc values for the same GC3 content suggested the role of translational selection. Mutational bias is suggested at synonymous position. Among optimal codons for translation, most were GC-ending. Seven codons (AGA, AGG, AUA, UAA, UAG, UCA and UGA) were found to have least occurrence in the entire genome and except stop codons all were A-ending (exception AGG). Most widely used codon-pair in the genome are G-ending or C-ending and A-ending or U-ending codons make pair with G-ending or C-ending codons. Amino acids which are largely distributed in T. elongatus tend to use G-ending or C-ending codons most frequently. Findings showed cumulative role of translational selection, translational accuracy and gene expression levels with mutational bias as key player in codon selection pattern of this organism.
authors: National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, Uttar Pradesh, India; Department of Biotechnology, Mewar University, Chittorgarh, Rajasthan, India.
authors: Ratna
authors: R
authors: Prabha
authors: National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, Uttar Pradesh, India.
authors: Dhananjaya P
authors: DP
authors: Singh
authors: Indian Agricultural Statistical Research Institute, Indian Council of Agricultural Research, Pusa, New Delhi 110012, India.
authors: Anil
authors: A
authors: Rai
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003062:Codon / Q000235:genetics*; D000458:Cyanobacteria / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data
chemical_list: D000596:Amino Acids; D003062:Codon
keywords: Thermosynechococcus elongatus; amino acids; bioinformatics; codon usage; codons; codon–pair context; gene expression levels; genome analysis; mutational bias; thermophile; thermophilic cyanobacteria; translational accuracy; translational selection