萱草海水胁迫相关WRKY转录因子密码子偏向性分析  

Analysis of codon bias in WRKY transcription factors related to seawater stress in Hemerocallis fulva

作　　者：桑娟 王艺程 李玺 张世杰 朱盛杰 席志俊 张琼 张志国 秦巧平 刘翔 SANG Juan;WANG Yicheng;LI Xi;ZHANG Shijie;ZHU Shengjie;XI Zhijun;ZHANG Qiong;ZHANG Zhiguo;QIN Qiaoping;LIU Xiang(School of Ecological Technology and Engineering,Shanghai Institute of Technology,Shanghai 201418,China;State Key Laboratory of Tree Genetics and Breeding,Chinese Academy of Forestry,Beijing 100091,China;Bureau of Agriculture and Rural Affairs of Datong City,Datong 037000,Shanxi,China)

机构地区：[1]上海应用技术大学生态技术与工程学院,上海201418 [2]中国林业科学研究院林木遗传育种全国重点实验室,北京100091 [3]山西省大同市农业农村委局,山西大同037000

出　　处：《应用技术学报》2024年第2期245-253,共9页Journal of Technology

基　　金：上海市农业农村委员会科技兴农项目(2019-02-08-00-08-F01107);大同黄花产业发展研究院科研合作项目(27220H220021);上海应用技术大学引进人才基金项目(YJ2019-25)资助。

摘　　要：在植物进化的过程中,不同物种的基因具有特定的密码子使用偏好性。WRKY基因家族在植物抗逆过程中扮演着重要角色。萱草是一种抗逆性极强的优秀园艺植物。为了深入探究萱草WRKY基因的密码子使用特征,采用CodonW和EMBOSS在线程序对海水胁迫诱导相关21条WRKY转录因子(HfWRKY)进行密码子分析。同时,利用Excel和Rstudio软件绘制中性分析图、ENc-plot图和PR2-plot图,旨在揭示HfWRKY基因的密码子使用规律。HfWRKY基因GC平均含量为48.31%,GC3平均含量为51.72%,这表明HfWRKY基因更倾向使用G/C结尾的密码子,且其密码子使用偏好性较弱。相对同义密码子分析显示,28个密码子的RSCU值>1,其中13个以A或T结尾,15个以G或C结尾。此外,有效密码子数的取值范围在46.54~59.64之间,密码子适应指数范围为0.158~0.274。通过中性分析、ENc-plot和PR2-plot图发现HfWRKY基因的密码子使用模式受到突变和自然选择等因素的影响。最后,鉴定出10个HfWRKY基因家族的最优密码子并证明其与抗性相关。本研究结果对于进一步挖掘HfWRKY基因家族在萱草在海水胁迫方面的作用和分子育种提供了理论依据。During the process of plant evolution,genes of different species exhibit specific codon usage biases.The WRKY gene family plays an important role in plant stress resistance.Hemerocallis fulva is an excellent horticultural plant with strong stress resistance.To further explore the codon usage characteristics of Hemerocallis fulva WRKY(HfWRKY)genes,the CodonW and EMBOSS online programs were employed to analyze 21 WRKY transcription factors related to seawater stress induction.Additionally,Excel and Rstudio software were utilized to generate neutrality analysis charts,ENc-plot charts,and PR2-plot charts,aiming to reveal the codon usage patterns of HfWRKY genes.The results showed that the average GC content of HfWRKY genes was 48.31%,while the average GC3 content was 51.72%,indicating that HfWRKY genes tend to use G/C-ending codons with a relatively weak codon usage bias.Relative Synonymous Codon Usage(RSCU)analysis revealed that 28 codons had RSCU values greater than 1,with 13 ending in A or T and 15 ending in G or C.Furthermore,the effective number of codons ranged from 46.54 to 59.64,and the codon adaptation index ranged from 0.158 to 0.274.Through neutrality analysis,ENc-plot,and PR2-plot charts,it was found that the codon usage patterns of HfWRKY genes were influenced by factors such as mutation and natural selection.Finally,10 optimal codons were identified in the HfWRKY gene family,demonstrating their association with resistance.The results of this study provide a theoretical basis for further exploring the role of the HfWRKY gene family in seawater stress resistance and molecular breeding in Hemerocallis fulva.

关 键 词：萱草 WRKY 转录因子 密码子偏向性 最优密码子 

分 类 号：Q751[生物学—分子生物学]