Bioinformatics Codon Usage Analysis of Chloroplast Genomes in Some Diploid Species and Comparison with Two Tetraploid Species of Cotton

Analysis of codon usage is very important to optimize the production of proteins in gene expression system. Gossypium spp. is the most important fiber crop in the modern world. In this research the complete nucleotide sequence of the chloroplast genomes of two wild cotton species was studied and analyzed using codon W software. Synonymous codon usage of 57 protein coding genes in chloroplast genome of G.thurberi and G.arboreum was analyzed to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. Correspondence analysis and method of effective number of codon as NC-plot were conducted to analyze synonymous codon usage. ENC Vs GC3 plot grouped majority of the analyzed genes on or just below the left side of the expected GC3 curve indicating the influence of base compositional constraints in regulating codon usage. According to the corresponding analysis, codon bias in the chloroplast genome of G.thurberi and G.arboreum are related to their gene length, mutation bias, gene hydropathic level of each protein, gene function and selection or gene expression only subtly affect codon usage. This study provided insights into the molecular evolution studies.