普通油茶叶绿体基因组密码子偏好性分析

王鹏良<sup>1; 3*</sup>; 杨利平<sup>2</sup>; 吴红英<sup>2</sup>; 农有良<sup>1</sup>; 吴双成<sup>1</sup>; 肖玉菲<sup>3</sup>; 覃子海<sup>3</sup>; 王华宇<sup>1; 2</sup>; 刘海龙<sup>3</sup>

引用本文:	王鹏良, 杨利平, 吴红英, 农有良, 吴双成, 肖玉菲, 覃子海, 王华宇, 刘海龙.普通油茶叶绿体基因组密码子偏好性分析[J].广西植物,2018,38(2):135-144.[点击复制]
	WANG Pengliang, YANG Liping, WU Hongying, NONG Youliang, WU Shuangcheng, XIAO Yufei, QIN Zihai, WANG Huayu, LIU Hailong.Condon preference of chloroplast genome in Camellia oleifera[J].Guihaia,2018,38(2):135-144.[点击复制]

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普通油茶叶绿体基因组密码子偏好性分析
王鹏良^1,3*, 杨利平², 吴红英², 农有良¹, 吴双成¹, 肖玉菲³, 覃子海³, 王华宇^1,2, 刘海龙³
1. 广西北部湾海洋生物多样性养护重点实验室, 钦州学院, 广西钦州 535011;2. 钦州市植物生物技术重点实验室, 广西钦州市林业科学研究所, 广西钦州 535099;3. 广西特色经济林培育与利用重点实验室, 广西壮族自治区林业科学研究院, 南宁 530002

摘要:

为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:密码子第三位GC含量为27.55%,ENC范围在35.23～56.67之间,平均值为46.09; RSCU值大于1.00的密码子数目为30个,其中29个第三位碱基以U或A结尾; 中性绘图表明GC₁₂与GC₃的相关系数为0.143,相关性不显著,回归系数为0.0573; 频数分布显示,55%基因的ENC比值集中分布在0～0.1,25%基因的ENC比值分布在0.1～0.2之间; 对应分析结果表明,第一向量轴占10.12%的差异,第二向量轴占9.36%的差异,其余两轴分别占7.97%和7.46%,前4轴累计差异为34.91%。中性绘图、ENC-plot和对应性分析均表明普通油茶叶绿体基因密码子偏好受突变作用,更多受选择的影响。最终取高表达优越密码子和高频密码子共有的CUU、AUU、GUU、GUA、UAA、CAA、AAA、GAC、GAA、CCU、ACU、GCU、GCA、UGU、CGU、AGU、UUG、GGU等18个密码子作为最优密码子。该研究结果为利用叶绿体基因工程技术改良普通油茶重要经济性状奠定了基础。

关键词: 普通油茶, 叶绿体, 密码子偏好, ENC, RSCU

DOI：10.11931/guihaia.gxzw201708001

分类号:Q943.2

文章编号:1000-3142(2018)02-0135-10

基金项目:国家自然科学基金(31460208); 钦州市科学研究与技术开发项目(201616804)[Supported by the National Natural Science Foundation of China(31460208); the Program of Science and Technology of Qinzhou(201616804)]。

Condon preference of chloroplast genome in Camellia oleifera

WANG Pengliang^1,3*, YANG Liping², WU Hongying², NONG Youliang¹, WU Shuangcheng¹, XIAO Yufei³, QIN Zihai³, WANG Huayu^1,2, LIU Hailong³

1. Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou 535011, Guangxi, China;2. Qinzhou Key Laboratory of Plant Biotechnology, Qinzhou Forestry Science Insititute, Qinzhou 535099, Guangxi, China;3. Guangxi Key Laboratory of Special Non-Wood Forest Cultivation and Utilization, Guangxi Zhuang Autonomous Region Forestry Science Institute, Nanning 530002, China 1. Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou 535011, Guangxi, China; 2. Qinzhou Key Laboratory of Plant Biotechnology, Qinzhou Forestry Science Insititute, Qinzhou 535099, Guangxi, China; 3. Guangxi Key Laboratory of Special Non-Wood Forest Cultivation and Utilization, Guangxi Zhuang Autonomous Region Forestry Science Institute, Nanning 530002, China

Abstract:

With the rapid development of the industry and increase of planting area of Camellia oleifera, the harvest was still affected by the factors such as the tolerance of disease, insect and drought as well as mating compatibility. Genetic engineering of chloroplast was an effective way to improve the important traits of plant. In order to improve the important traits of C. oleifera, it was necessary to carry out the analysis on codon preference of its chloroplast genome. The whole genome sequence of chloroplast in C. oleifera taken as raw material, 51 CDS who were longer than 300 bps, started with ATG and not repeated were screened for future analysis. The codon preference was conducted by the CodonW software. The results indicated that the GC content of the third base of genetic code was 27.55% and effective number of codons ranged from 35.23 to 56.67 with an average of 46.09 and then 29 codons of 30 whose RSCU were more than 1 ended with A or U. Neutral plot analysis showed the correlation between GC₁₂ and GC₃ was not significant and the coefficient of correlation and regression was 0.143 and 0.057 3, respectively. Frequency analysis showed 55% and 25% of the ENC ratio of genes focused on the region of 0-0.1 and 0.1-0.2. Correspondence analysis indicated the first axis accounted for 10.12 variation and the rested three axises accounted for 9.36%, 7.97% and 7.46% and the first four axises accounted for 34.91% in total. All the methods used in this study showed that codon preference was affected by not only mutation and but also selection. Finally the 18 optimal codons including CUU, AUU, GUU, GUA, UAA, CAA, AAA, GAC, GAA, CCU, ACU, GCU, GCA, UGU, CGU, AGU, UUG, GGU were determined. This work provides plenty of information for improving important traits of C. oleifera utilizing the genetic engineering of chloroplast.

Key words: Camellia oleifera, chloroplast, codon preference, effective number of codon, relative synonymous codon usage