Mutation pressure and natural selection on codon usage in chloroplast genes of two species in <i>Pisum</i> L. (Fabaceae: Faboideae)

This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of <i>Pisum viz</i>. <i>P. fulvum</i> and <i>P. sativum</i> and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of <i>Pisum</i> chloroplast genomes. It was found that GC content was lower than AT content in the genes. Low synonymous codon usage order (SCUO) values of genes indicated low CUB in chloroplast genes of <i>Pisum</i> species. Heatmaps showed positive correlations of GC3 with all the GC and AT ending codons. Neutrality plot analysis revealed that natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes in these two taxa. Positive correlation between SCUO and mRNA free energy (mFE) suggested that higher energy release by entire mRNA was related to high degree of CUB. Further, highly significant (<i>p</i>