| 摘要: |
| 为了分析美丽梧桐、云南梧桐叶绿体基因组密码子的使用偏性,该研究通过筛选美丽梧桐、云南梧桐叶绿体基因组中各52条蛋白编码序列,并利用CodonW、CUSP和SPSS软件对其密码子使用模式及偏性进行了分析。结果表明:(1)美丽梧桐、云南梧桐的GC含量分别为38.12%、38.05%,表明叶绿体基因组内富含A/T碱基。(2)有效密码子数(ENC)范围为36.91～56.46、36.55～58.04,表明多数密码子偏性较弱。(3)相对同义密码子(RSCU)分析显示,RSCU>1的密码子各有29个,其中28个以A、U结尾。(4)中性绘图显示,GC3与GC12的相关性不显著,回归曲线斜率分别为0.195和0.304,说明密码子偏好性主要受到自然选择的影响。(5)ENC-plot分析中大部分基因分布于曲线的周围和下方,ENC比值多分布于-0.04～0.10之间,表明突变会影响密码子偏性的形成。此外,17、18个密码子分别被鉴定为美丽梧桐、云南梧桐的最优密码子。以上结果说明美丽梧桐、云南梧桐叶绿体基因组的密码子使用偏性可能受选择和突变共同作用,且使用模式较为相似,但具有一定的差异,可能与适应环境的进化机制有关。 |
| 关键词: 美丽梧桐, 云南梧桐, 叶绿体基因组, 密码子偏性, 最优密码子 |
| DOI：10.11931/guihaia.gxzw201811035 |
| 分类号:Q943.2 |
| 文章编号:1000-3142(2020)02-0173-11 |
| 基金项目:国家自然科学基金(31700196); 广西科学院基本业务费项目(2017YJJ23008); 广西植物研究所基本业务费项目(GZY16003,GZY17008)[Supported by the National Natural Science Foundation of China(31700196); Fundamental Research Foundation of Guangxi Academy of Sciences(2017YJJ23008); Fundamental Research Foundation of Guangxi Institute of Botany(GZY16003, GZY17008)]。 |
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| Codon usage bias of chloroplast genome from two species of Firmiana Marsili |
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LU Qifeng, LUO Wenhua, HUANG Zhihuan*
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Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, Guangxi, China
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| Abstract: |
| In order to analyze the codon usage patterns of the chloroplast genome of Firmiana pulcherrima and F. major. Fifty-two genes selected from chloroplast genome(Cp genome)of these two species were analyzed using CodonW, CUSP and SPSS software. The results showed that:(1)GC content in Firmiana pulcherrima was 38.12%, and that in F. major was 38.05%, suggesting that A/T base was rich in chloroplast genome.(2)The effective number of codons in F. pulcherrima ranged from 36.91 to 56.46, and that in F. major ranged from 36.55 to 58.04, meaning the codon bias was weak in F. pulcherrima and F. major.(3)Both F. pulcherrima and F. major had 29 codons with relative synonymous codon usage(RSCU)greater than 1 and 28 codons ending with A and U base.(4)Neutrality plot showed that there was not significant correlation between GC3 and GC12, and the regression slope was 0.195 in F. pulcherrima, and 0.304 in F. major, suggesting that codon bias was mainly affected by natural selection.(5)ENC-plot analysis showed that most of genes fell below and followed the standard curve, and ENC ratio of most genes ranged from -0.04 to 0.10, suggesting that the mutation also affected the formation of codon bias in F. pulcherrima and F. major. In addition, 17 codons were identified as optimal codons in F. pulcherrima, and 18 codons in F. major. We suggest that the codon usage bias of F. pulcherrima and F. major are formed under effect of mutation and selection. Although the codon usage pattern of F. pulcherrima and F. major are very similar, there are some differences, which may be related to the evolutionary me-chanism of adaptive environment. |
| Key words: Firmiana pulcherrima, F. major, chloroplast genome, codon usage bias, optimal codons |
