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

Abstract

This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of Pisum viz. P. fulvum and P. sativum and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of Pisum 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 Pisum 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 (p < .01) negative correlation was found between parameters in pair i.e. mFE-GC, mFE-GC1, mFE-GC2 and mFE for entire mRNA-GC3. This pointed out that higher GC content might have influenced lesser energy release by mRNA molecules of chloroplast genes.

Keywords:

• Codon usage bias
• chloroplast gene
• Pisum fulvum
• Pisum sativum
• Fabaceae

Acknowledgements

We are thankful to Assam University, Silchar, Assam India for providing the necessary facilities to carry out the work. The authors are also thankful to Dr. Petr Smýkal, Associate Professor, Department of Botany, Palacky University in Olomouc, Slechtitelu, Olomouc, Czech Republic for his valuable suggestions and also for providing a few relevant literature through personal contact.

Disclosure statement

The authors declare that there is no conflict of interests in the manuscript.