Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India.
Planta. 2020 Sep 28;252(4):67. doi: 10.1007/s00425-020-03470-7.
The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species 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 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. 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 across Oryza species. 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 across Oryza species.
稻属叶绿体基因的密码子使用偏性较低，富含 AT。不同稻种的密码子使用模式不同，主要受突变压力和自然选择的影响。密码子使用偏性（CUB）是指基因编码序列中某些同义密码子的使用频率不平等，表现出物种特异性。我们研究了 18 个稻种叶绿体（cp）蛋白编码基因的密码子使用模式及其影响 CUB 的因素，因为之前没有相关工作的报道。核苷酸组成分析表明，不同稻种 cp 基因的总 GC 含量低于 50%，即稻 cp 基因富含 AT。同义密码子使用顺序（SCUO）表明，不同稻种的 cp 基因 CUB 较弱。在第三密码子位置，整体核苷酸与其组成之间存在高度显著的相关性，表明突变压力和自然选择可能都影响 CUB。对应分析（COA）表明，不同稻种的密码子使用模式存在差异。在中性图谱中，GC3 分布范围较窄，所有图谱中都有一些点呈对角线分布，表明自然选择和突变压力可能影响了 CUB。回归线的斜率小于 0.5，这进一步证明了自然选择可能发挥了主要作用，而突变压力在塑造 cp 基因的 CUB 方面作用较小。不同稻种的 cp 基因受到的突变压力和自然选择的程度不同。
