| 楸树叶绿体基因组密码子偏性分析 |
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| 引用本文： | 李凤,辛静,辛雅萱,肖遥,屈亚亚,王军辉,麻文俊,辛培尧.楸树叶绿体基因组密码子偏性分析[J].南方农业学报,2021,52(10):2735-2743. |
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| 作者姓名： | 李凤 辛静 辛雅萱 肖遥 屈亚亚 王军辉 麻文俊 辛培尧 |
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| 作者单位： | 1 西南林业大学国家林业和草原局西南风景园林工程技术研究中心/西南地区生物多样性保育国家林业和草原局重点实验室, 昆明 650224;2 中国林业科学研究院林业研究所/林木遗传育种国家重点实验室/国家林业和草原局林木 培育重点实验室/楸树国家创新联盟, 北京 100091 |
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| 基金项目： | 中央级公益性科研院所基本科研业务费专项（CAFYBB2017ZA001-8） |
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| 摘 要： | 【目的】分析楸树叶绿体基因组密码子使用偏性，为楸树乃至梓属植物叶绿体基因组学、物种进化特征及遗传多样性分析等研究提供理论依据。【方法】利用Codon W 1.4.2及EMBOSS expiorer的cusp和chips软件对51个楸树叶绿体基因的编码区（CDS）序列进行密码子相关参数、中性绘图、ENC-plot和PR2-plot等分析，并通过构建高、低表达偏性基因库，以ENC值和RSCU值为参考标准，最终筛选最优密码子。【结果】51个基因密码子的平均GCall含量为38.48%，密码子不同位置GC含量为:GC1（47.03%）>GC2（39.93%）>GC3（28.09%），说明第3位的GC并非均匀分布；ENC为34.93~56.50，平均为46.87。GC2与GC1呈极显著正相关（P<0.01），而GC3与GC1和GC2无显著正相关（P>0.05）；ENC与GCall、GC1、GC3和N均呈显著正相关（P<0.05，下同）；密码子数（N）与GC3和ENC呈显著正相关。RSCU>1的密码子共有30个，其中，以A或U结尾的密码子有29个。中性绘图分析结果显示，GC3与GC12相关系数为0.0188，二者无显著相关性，回归系数为0.143。ENC-plot分析结果显示，大部分基因偏离了ENC预期标准曲线，少数分布在预期曲线附近；有7个密码子分布在GC3含量-0.05~0.15区间，其余区间共有44个密码子，而这44个基因离ENC标准曲线较远。PR2-plot分析结果显示，落在中线上的基因较少，平面图右下方的基因分布较多，表明在各碱基使用频率方面存在偏性，即T>A，G>C。各碱基使用频率存在偏性（T>A，G>C），说明基因组密码子的偏性更多受选择效应的影响。最终筛选出7个为最优密码子UUU、CUU、CCU、AAA、GAU、CGA和GGU。【结论】楸树叶绿体基因组密码子偏性较弱，偏好使用A或U结尾的密码子，主要受选择压力的影响，受突变等其他因素影响较小。
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| 关 键 词： | 楸树 叶绿体基因组 密码子偏好性 最优密码子 |
| 收稿时间： | 2021-05-20 |
Codon usage bias of chloroplast genome in Catalpa bungei C. A. Mey. |
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| LI Feng,XIN Jing,XIN Ya-xuan,XIAO Yao,QU Ya-ya,WANG Jun-hui,MA Wen-jun,XIN Pei-yao.Codon usage bias of chloroplast genome in Catalpa bungei C. A. Mey.[J].Journal of Southern Agriculture,2021,52(10):2735-2743. |
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| Authors: | LI Feng XIN Jing XIN Ya-xuan XIAO Yao QU Ya-ya WANG Jun-hui MA Wen-jun XIN Pei-yao |
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| Abstract: | 【Objective】Analyzed the codon usage bias of Catalpa bungei C. A. Mey. chloroplast genome to provide theoretical basis for the research of C. bungei and even Catalpa chloroplast genomics, species evolution characteristics and genetic diversity analysis.【Method】Codon correlation parameters, neutral plots, ENC-plot and PR2-plot were analyzed for 51 chloroplast gene coding regions(CDS) sequences of C. bungei by Codon W 1.4.2 and cusp and chips of EMBOSS expiorer. And through the constitutive high and low expression-biased gene library, ENC value and RSCU value were used as reference criteria to screen the optimal codon.【Result】The average GCall content of 51 gene codons was 38.48%, and GC content at different positions of codons was as follows:GC1(47.03%) >GC2(39.93%) >GC3(28.09%), indicating that GC at the third position was not evenly distributed. ENC ranged from 34.93 to 56.50, with an average of 46.87. GC2 was extremely significantly positively correlated with GC1(P<0.01), while GC3 was not significantly positively correlated with GC1 and GC2(P>0.05). ENC was significantly positively correlated with GCall, GC1, GC3 and N(P<0.05, the same below). The codon number(N) was positively correlated with GC3 and ENC. There were 30 codons with RSCU>1, among which 29 codons ended in A or U. Neutral plot analysis results showed that the correlation coefficient between GC3 and GC12 was 0.0188, and there was no significant correlation between them, and the regression coefficient was 0.143. ENC-plot analysis showed that most of the genes deviated from the ENC expected standard curve, and a few were distri-buted near the expected curve. There were 7 codons distributed in the range of GC3 content from -0.05 to 0.15, and there were 44 codons in the other regions, which were far from the ENC standard curve. PR2-plot analysis results showed that fewer genes fell on the middle line, and more genes were distributed in the lower right part of the graph, indicating that there was a bias in the use frequency of each base, namely T>A, G>C.There was bias(T>A, G>C) in the use frequency of each base, indicating that the bias of the genome codon was more influenced by the selection effect. Finally, 7 optimal codons were selected as UUU, CUU, CCU, AAA, GAU, CGA and GGU.【Conclusion】The chloroplast genomes of C. bungei show weak codon bias, preferring to use codons ending in A or U, which is mainly affected by selection pressure and less affected by mutation and other factors. |
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