MAIN CONCLUSION 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.

中文翻译：

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水稻叶绿体基因密码子使用偏倚分析

主要结论 水稻叶绿体基因的密码子使用偏倚低且AT丰富。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。密码子使用偏差 (CUB) 是同义密码子的不平等使用，其中一些密码子在基因的编码序列中比其他密码子更偏好。它显示了物种特有的属性。我们研究了 18 个稻种中密码子使用模式和影响蛋白质编码叶绿体 (cp) 基因 CUB 的因素，因为尚未报告任何工作。核苷酸组成分析表明，不同品种水稻中cp基因的总体GC含量低于50%，即水稻cp基因AT丰富。同义密码子使用顺序（SCUO）表明CUB在不同稻种的cp基因中较弱。在第三个密码子位置的总核苷酸与其成分之间观察到高度显着的相关性，这表明突变压力和自然选择都可能影响 CUB。对应分析 (COA) 显示，密码子使用模式在稻种之间存在差异。在中性图中，GC3 的分布范围很窄，并且一些点在所有图中呈对角线分布，这表明自然选择和突变压力可能影响了 CUB。回归线的斜率 < 0.5，增强了我们的推断，即自然选择可能起主要作用，而突变压力在塑造 cp 基因的 CUB 中起次要作用。对 cp 基因的突变压力和自然选择的大小因稻种而异。