普通野生稻线粒体蛋白质编码基因密码子使用偏好性的分析

Analysis of codon usage bias in the mitochondrial protein-coding genes of Oryza rufipogon

以普通野生稻(Oryza rufipogon Griff.)线粒体基因组为对象,分析其蛋白质编码基因的密码子使用特征及与亚洲栽培稻(O. sativa L.)的差异,探讨其密码子偏性形成的影响因素和进化过程。结果显示:普通野生稻线粒体基因组编码序列第1、第2和第3位碱基的GC含量依次为49.18%、42.67%和40.86%;有效密码子数(Nc)分布于45.32～61.00之间,其密码子偏性较弱; Nc值仅与GC_3呈显著相关,密码子第3位的碱基组成对密码子偏性影响较大;第1向量轴上显示9.91%的差异,其与GC_(3s)、Nc、密码子偏好指数(CBI)和最优密码子使用频率(Fop)的相关性均达到显著水平;而GC_3和GC_(12)的相关性未达到显著水平。因此,普通野生稻线粒体基因组密码子的使用偏性主要受自然选择压力影响而形成。本研究确定了21个普通野生稻线粒体基因组的最优密码子,大多以A或T结尾,与叶绿体密码子具有趋同进化,但是与核基因组具有不同的偏好性。同义密码子相对使用度(RSCU)、PR2偏倚分析和中性绘图分析显示,普通野生稻线粒体基因功能和其密码子使用密切相关,且线粒体密码子使用在普通野生稻、粳稻(O. sativa L. subsp. japonica Kato)和籼稻(O. sativa L. subsp.indica Kato)内具有同质性。

The mitochondrial genome of Oryza rufipogon Griff. was used to analyze the codon usage characteristics of protein-coding genes and the differences with Asian cultivated rice ( O.sativa L.), and to explore the influencing factors of codon usage bias and codon evolution. Results showed that the effective number of codons (Nc) ranged from 45. 32 to 61. 00, indicating that codon bias was weak. GC content at the three codon positions was 49. 18%, 42. 67%, and 40. 86%. The Nc value was significantly correlated with GC 3 but not with GC 1 or GC 2 , suggesting that base composition at the third codon position had a greater effect on codon bias. In the corresponding analysis, the first axis showed 9. 91% variation and was significantly correlated with GC 3s , Nc, CBI, and Fop. Furthermore, GC 12 showed non-significant correlation with GC 3 . Codon bias in the mitogenome of O. rufipogon was mainly affected by natural selection. In addition, we identified 21 optimal codons, with most of the preferred synonymous codons ending in A or T. The mitochondrial codons showed convergent evolution with Oryza chloroplast codons, but different preferences with the nuclear genome. Based on neutrality plot analysis, PR2-plot analysis, and RSCU analysis, we found no significant differences among the three Oryza species. Our results also confirmed homogeneity in mitochondrial codon usage among the three Oryza species.