Analysis of codon usage bias of chloroplast genes in Oryza species Codon usage of chloroplast genes in Oryza species

Main conclusion The codon usage bias in chloroplast genes ofOryzaspecies was low and AT rich. The pattern of codon usage was different amongOryzaspecies and mainly influenced by mutation pressure and natural selection. Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18Oryzaspecies as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species ofOryzawas lower than 50%, i.e.,Oryzacp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of differentOryzaspecies. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed acrossOryzaspecies. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in shaping the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied acrossOryzaspecies.