Codon usage bias and its influencing factors in the chloroplast genome of Macadamia integrifolia Maiden & Betche
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摘要: 为确定澳洲坚果光壳种（Macadamia integrifolia Maiden&Betche）叶绿体基因组密码子偏好性形成的主要影响因素，本研究通过其叶绿体基因组的51条蛋白编码序列，系统分析其密码子的使用模式及其特征。密码子偏好性参数分析结果显示，叶绿体基因密码子3位碱基的GC含量次序为GC1 > GC2 > GC3；有效密码子数ENC均值为48.80（>阈值45），其密码子偏性较弱；GC3与ENC呈显著相关，影响其偏好性。中性绘图分析结果表明，GC12与GC3的相关系数和回归曲线斜率分别为0.186和0.265，两者相关性不显著。ENC-plot分析发现大部分基因接近于标准曲线，其ENC比值位于-0.05~0.05，与期望值差异较小。PR2-plot偏倚分析表明密码子第3位碱基的使用频率不均等，嘧啶T/C高于嘌呤A/G。RSCU分析发现29个高频密码子、19个高表达密码子及16个最优密码子中绝大多数偏好使用以A或U结尾。系统进化分析结果显示，澳洲坚果光壳种和三叶澳洲坚果（M.ternifolia F.Mueller）的亲缘关系最近。研究结果说明，作为主要因素的自然选择和碱基突变相对均衡地共同影响澳洲坚果光壳种叶绿体基因组较弱的密码子使用偏好性，且影响其偏好性的密码子第3位碱基偏好使用A或U。Abstract: Codon usage bias of 51 genes from the chloroplast genome of Macadamia integrifolia Maiden & Betche was analyzed to determine the main factors affecting the formation of codon bias. The GC content at different codon positions in the chloroplast genes was GC1 > GC2 > GC3, and GC3 was significantly correlated with effective number of codons (ENC) (mean value 48.80 > threshold 45), indicating that the third codon position had direct impact on weak codon bias in the chloroplast genome of M. integrifolia. Neutral-plot analysis showed that there was no significant correlation between GC12 and GC3, with a correlation coefficient and regression slope of 0.186 and 0.265, respectively. ENC-plot analysis showed that most genes were located around the standard curve, and their ENC ratios were distributed between -0.05 and 0.05, suggesting that the differences between actual and expected ENC were small. PR2-plot analysis revealed that the third codon position was biased, where pyrimidine T/C was used more frequently than purine A/G. Relative synonymous codon usage (RSCU) analysis showed that most of the 29 high-frequency codons, 19 high-expression codons, and 16 optimal codons preferentially ended with A or U. Phylogenetic analysis showed that the relationship between M. integrifolia and M. ternifolia was similar. These results suggest that natural selection and base mutation are the main factors influencing weak codon bias in the chloroplast genome of M. integrifolia, and the third codon base, as another influencing factor, prefers to use A or U.
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