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>

本研究旨在聚焦两种豌豆属（*Pisum*）物种，即褐豌豆（*P. fulvum*）和普通豌豆（*P. sativum*）的叶绿体基因密码子使用偏好性（codon usage bias, CUB）模式，并解析影响其密码子使用偏好性的关键因素。本研究借助生物信息学工具，对豌豆属叶绿体基因组的蛋白编码序列开展密码子使用模式分析。研究发现，上述基因的GC含量低于AT含量。基因的同义密码子使用顺序（synonymous codon usage order, SCUO）值偏低，表明豌豆属物种叶绿体基因的密码子使用偏好性较弱。热图分析结果显示，GC3与所有以GC、AT结尾的密码子均呈正相关。中性绘图分析表明，相较于突变压力，自然选择在塑造这两个类群的叶绿体基因密码子使用偏好性的过程中发挥了更为主导的作用。同义密码子使用顺序与mRNA自由能（mRNA free energy, mFE）之间呈显著正相关，这提示完整mRNA释放的能量越高，其密码子使用偏好性程度也越高。进一步分析显示，极显著（*p*