黄皮转录组密码子使用偏好性分析  

Analysis of Codon Usage Bias in Clausena lansium Transcriptome

作　　者：陆育生 彭程 陈喆 常晓晓[1] 邱继水[1] 林志雄[1] 潘建平[1] Lu Yusheng;Peng Cheng;Chen Zhe;Chang Xiaoxiao;Qiu Jishui;Lin Zhixiong;Pan Jianping(Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization（MOA）,Guangdong Province Key Laboratary of Tropical and Subtropical Fruit Tree Research,Institute of Fruit Tree Research,Guangdong Academy of Agricultural Sciences,Guangzhou,510640)

机构地区：[1]广东省农业科学院果树研究所广东省热带亚热带果树研究重点实验室农业部南亚热带果树生物学与遗传资源利用重点实验室,广州510640

出　　处：《分子植物育种》2018年第18期5904-5913,共10页Molecular Plant Breeding

基　　金：广东省科技计划项目(2016B020201004);国家自然科学基金项目(31501729);广东省优稀水果产业技术体系项目(2016LM1071);农业部热带作物种质资源保护项目(16RZZY-20);广东省农业科学院院长基金项目(201605)共同资助

摘　　要：为全面了解黄皮(Clausena lansium)表达基因的密码子使用特点,以转录组测序获得的12 696条编码蛋白基因序列为数据来源,利用CodonW 14.4软件对其密码子碱基组成以及有效密码子数(effective number of codon, ENC)、同义密码子相对使用频率(relative frequency of synonymous codon, RFSC)等密码子使用参数进行计算和统计,发现黄皮表达基因密码子的平均GC含量为0.448,同义密码子第3位核苷酸的平均GC含量(GC3S)为0.400。表达基因整体的ENC取值为56.5,其中绝大部分的ENC值大于35,说明黄皮表达基因密码子使用偏好性程度整体水平较低。通过高频密码子分析法确定了GCU、AGA、AAU、GAU、AUU、UUU、UCU、CAU、CUU、UUG和GUU 11个高频密码子。将黄皮的密码子使用频率与人、小鼠、果蝇、酵母、大肠杆菌5种模式生物以及拟南芥、水稻、葡萄、草莓4种不同类型植物进行比较,发现其与果蝇和大肠杆菌存在较大差异,而与拟南芥和葡萄基本一致。以上研究结果对黄皮基因合适表达系统的选择以及外源基因在黄皮中的高效表达具有重要指导意义。In order to fully understand the codon usage pattern of wampee（Clausena lansium）, a total of 12 696 coding DNA sequences（CDS） acquired from the wampee transcriptome data were used for the analysis of codon composition and usage parameters including the effective number of codon（ENC） and relative frequency of synonymous codon（RFSC） by using CodonW 14.4 software. The results indicated that the GC content of wampee genes was 0.448, and the GC content of the third nucleotide of synonymous codon was 0.400. The ENC of whole genes was 56.5, and the majority of the ENC values were over 35, which suggested the codon usage bias was lower in the CDSs of Clausena lansium. Eleven high-frequency codons including GCU, AGA, AAU, GAU, AUU, UUU, UCU,CAU, CUU, UUG and GUU were revealed by high-frequency codon analysis. When the frequency of codon usage of Clausna lansium was compared to five model organisms including Homo sapiens, Mus musculus, Drosophila melanogaster, Saccharomyces cerevisiae, Escherichia coli, and four different plants including Arabidopsis thaliana,Oryza sativa, Vitis vinifera and Fragaria ananassa, it was found that the codon usage bias was identical betweenClausna lansium and Arabidopsis thaliana, Vitis vinifera, while considerably different between Clausna lansium and Drosophila melanogaster, Escherichia coli. The above results would provide an important guidance for selecting appropriate host expression systems for Clausena lansium genes and increasing the expression efficiency of exogenous genes in Clausena lansium.

关 键 词：黄皮 转录组 密码子用法 高频密码子 密码子偏好性 

分 类 号：S666.6[农业科学—果树学]