20种千屈菜科植物rbcL基因密码子使用偏好性分析  

Codon usage bias analysis of rbcL genes of 20 Lythraceae species

作　　者：郑钢[1,2,3] 顾翠花[1,2,3] 林琳 王杰[1,2,3] ZHENG Gang;GU Cuihua;LIN Lin;WANG Jie(College of Landscape Architecture,Zhejiang A&F University,Hangzhou 311300,Zhejiang,China;Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants,Zhejiang A&F University,Hangzhou 311300,Zhejiang,China;Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants,Zhejiang A&F University,Hangzhou 311300,Zhejiang,China)

机构地区：[1]浙江农林大学风景园林与建筑学院,浙江杭州311300 [2]浙江农林大学浙江省园林植物种质创新与利用重点实验室,浙江杭州311300 [3]浙江农林大学南方园林植物种质创新与利用国家林业和草原局重点实验室,浙江杭州311300

出　　处：《浙江农林大学学报》2021年第3期476-484,共9页Journal of Zhejiang A&F University

基　　金：浙江省自然科学基金资助项目(LY21C160001)。

摘　　要：【目的】分析千屈菜科Lythraceae植物rbcL基因密码子使用特性,明确密码子偏好性的影响因素,筛选rbcL基因异源表达和遗传转化的合适受体。【方法】从美国国家生物技术信息中心(NCBI)获取20种千屈菜科植物的rbcL基因全长编码区序列(CDS)数据,运用CodonW、EMBOSS和DAMBE软件获取基因碱基组成和密码子使用偏好性的相关参数,分析该类植物叶绿体rbcL基因使用密码子的偏倚性及其影响因素。【结果】千屈菜科植物rbcL基因GC含量(GC)为0.425~0.437,密码子第3位碱基GC含量(GC3s)为0.275~0.300。GC3s、GC与有效密码子数(ENC)显著相关(P<0.01);ENC-GC3s散点图分析、中性绘图分析、奇偶偏差分析均表明:相较于突变压力,自然选择压力对千屈菜科植物rbcL基因密码子使用偏好性的影响更大。基于同义密码子相对使用度的系统聚类与CDS邻接树结果部分一致。与千屈菜科rbcL基因密码子平均使用频率相比,大肠埃希菌Escherichia coli、酵母Saccharomyces cerevisiae、拟南芥Arabidopsis thaliana、烟草Nicotiana tabacum和番茄Solanum lycopersicum分别存在28、26、20、19和17个使用频率相差较大的密码子。【结论】千屈菜科植物rbcL基因碱基组成上更倾向于选择A/T碱基,且偏好使用末端A/T碱基的密码子;rbcL基因密码子使用偏好性受多种因素共同作用,但自然选择压力是最主要因素;密码子偏好性的系统聚类可为系统发育研究提供补充;酵母更适合作为千屈菜科植物rbcL基因异源表达受体,番茄更适合作为rbcL基因遗传转化和功能研究的受体材料。[Objective] With an analysis of the codon usage characteristics of the rbcL genes in Lythraceae species, this study is aimed to clarify the influencing factors of codon bias, and screen the optimal receptor for heterologous expression and genetic transformation. [Method] After rbcL gene CDS of 20 Lythraceae species were obtained from NCBI, CodonW, EMBOSS, and DAMBE software were utilized to compute relevant parameters of gene base composition and codon usage bias before an analysis is conducted of the usage bias ofsuch genes and its incluencing factors using SPSS and Origin software. [Result] The GC content of the rbc L gene from Lythraceae species ranged from 0.425 to 0.437, with GC3 s being 0.275 to 0.300 and there was a significant correlation between GC3 s, GC, and ENC(P<0.01). As was shown in the analysis of ENC-GC3 s plot,the neutral plot and PR2, natural selection pressure affected the codon usage bias of the rbc L gene from Lythraceae species more heavily than mutation pressure. The result of clustering analysis based on RSCU is partially consistent with that of the neighbor-joining tree based on CDS. Compared with the average codon usage frequency of the rbc L gene from the 20 Lythraceae species, Escherichia coli, Saccharomyces cerevisiae,Arabidopsis thaliana, Nicotiana tabacum, and Solanum lycopersicum possessed 28, 26, 20, 19 and 17 codons,respectively, with significant differences in usage frequency. [Conclusion] In terms of the base composition of the rbc L gene from 20 Lythraceae species, there was a tendency towards A/T bases and codons with A/T base at ther termonal were generally preferred. Also, of all the factors having an influence on codon bias, natural selection pressure was the most important one. Systematic clustering is a good complement for phylogenetic analysis. S. cerevisiae is more suitable as a heterologous expression receptor, while S. lycopersicum is more suitable to act as a receptor material for genetic transformation and function research of rbc L gene.

关 键 词：碱基组成 选择压力 突变压力 聚类分析 受体 

分 类 号：S718.3[农业科学—林学]