| 引用本文: | 原晓龙,李云琴,张劲峰,王毅.降香黄檀叶绿体基因组密码子偏好性分析[J].广西植物,2021,41(4):622-630.[点击复制] |
| YUAN Xiaolong, LI Yunqin, ZHANG Jinfeng, WANG Yi.Analysis of codon usage bias in the chloroplast genome of Dalbergia odorifera[J].Guihaia,2021,41(4):622-630.[点击复制] |
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| 摘要: |
| 为了解降香黄檀叶绿体基因组密码子使用模式,该文利用CodonW1.4.2和在线软件CUSP对降香黄檀叶绿体基因组中的52条基因编码序列密码子进行中性绘图、ENC-plot和PR2-plot分析。结果表明:降香黄檀叶绿体基因组密码子的3个位置上GC含量依次为GC1(46.01%)>GC2(38.98%)>GC3(27.80%)。有效密码子数(ENC)范围为37.66～54.43,及ENC值>45的有37个;RSCU>1的密码子有29个,其中16个以U结尾、12个以A结尾。这些说明其偏好以A和U结尾,且偏性较弱。中性绘图分析显示GC12与GC3的相关系数为0.250,相关性不显著,回归系数为0.394;ENC-plot分析显示ENC比值位于-0.05～0.05区间外的基因有38个;PR2-plot分析说明在碱基的使用频率方面,U>A、G>C,说明降香黄檀叶绿体基因组密码子偏好性主要受选择的影响;19个密码子被确定为最优密码子。该研究为降香黄檀叶绿体基因工程、遗传多样性分析等研究提供了科学参考依据。 |
| 关键词: 降香黄檀,叶绿体基因组,密码子偏好性,选择 |
| DOI：10.11931/guihaia.gxzw201906012 |
| 分类号:Q755 |
| 文章编号:1000-3142(2021)04-0622-09 |
| 基金项目:国家自然科学基金(31860177);云南省林业科学院热带亚热带珍贵用材树种研发省创新团队(2017HC024)[SupportedbytheNationalNaturalScienceFoundationofChina(31860177);ProvincialInnovationGroupofR&DofPreciousTropicalandSubtropicalTimberSpeciesinYunnanAcademyofForestry(2017HC024)]。 |
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| Analysis of codon usage bias in the chloroplast genome of Dalbergia odorifera |
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YUAN Xiaolong, LI Yunqin, ZHANG Jinfeng, WANG Yi*
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Yunnan Key Laboratory of Forestry Plant Cultivation and Utilization, State Forestry and Grassland Administration Key Laboratory of Yunnan
Rare and Endangered Species Conservation and Propagation, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
Yunnan Key Laboratory of Forestry Plant Cultivation and Utilization, State Forestry and Grassland Administration Key Laboratory of Yunnan
Rare and Endangered Species Conservation and Propagation, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
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| Abstract: |
| To comprehend the codon usage pattern of chloroplast genome in Dalbergia odorifera, the 52 coding DNA sequences were analyzed to obtain to the results of neutrality plot, ENC-plot and PR2-plot analysis using Codon W 1.4.2 and online software CUSP in the present study. The results were as follows: The GC content in the three positions of codons from the chloroplast genome of D. odorifera was GC1(46.01%)>GC2(38.98%)>GC3(27.80%)successively. The range of effective number codon was from 37.66 to 54.43, and there were 37 genes when ENC value was greater than 45, and there were 29 genes when RSCU value was greater than 1, including 16 genes ending with U and 12 genes ending with A. These suggest that the codons prefer ends with A and U, and have a weak bias. The neutrality plot showed that there was no significant correlation between GC3 and GC12, the correlation coefficient was 0.250, and the regression coefficient was 0.394; ENC-plot analysis revealed that there were 38 genes which ENC ratio located beyond the section from -0.05 to 0.05; PR2-plot analysis showed that U>A and G>C in the base usage frequency. These all illustrated that the codon usage bias in the chloroplast genome of D. odorifera was mainly affected by mutation; 19 codons were identified as the optimal codon. The present study could be useful in the chloroplast genetic engineering and genetic diversity analysis of D. odorifera. |
| Key words: Dalbergia odorifera, chloroplast genome, codon usage bias, selection |
