番茄WRKY转录因子密码子偏性分析

Analysis of Codon Usage Bias of WRKY Transcription Factors in Tomato

WRKY基因家族在响应植物发育和生理过程、多种应激反应中发挥着重要作用。为揭示番茄WRKY基因的特性和密码子使用模式,本研究通过CodonW、CUSP和SPSS软件对番茄81个WRKY基因密码子使用偏性进行分析。结果表明:WRKY基因平均GC含量为39.33%,GC3平均含量为31.80%,表明WRKY基因密码子倾向以A或T(U)结尾;相对同义密码子(RSCU)分析显示,RSCU>1的密码子有27个,其中25个以A、U结尾;有效密码子数(ENC)和密码子适应指数(CAI)范围分别为35.77~55.93和0.13~0.28,表明密码子偏性较弱且WRKY基因表达水平较低;中性分析、ENC和PR2作图分析发现WRKY基因密码子使用模式受碱基组成、突变和自然选择压力的影响。此外,只有1个密码子鉴定为WRKY基因最优密码子。该研究结果为番茄WRKY基因转基因研究过程中密码子优化提供了理论支持。

The WRKY gene family plays an important role in diverse stress responses,developmental,and physiological processes.In order to understand the codon usage patterns of the WRKY gene family in tomato(Solanum lycopersicum),eighty-one WRKY genes from Solanum lycopersicum,were analyzed using CodonW,CUSP and SPSS software.The results showed that the average GC content of WRKY genes was 39.33%,and the average GC3 content was 31.80%,suggesting that WRKY gene family codons were more preferred to end with A or T(U).There were 27 codons with relative synonymous codon usage(RSCU)greater than 1 and 25 codons ending with A and U base.The effective number of codons(ENC)and codon adaptation index(CAI)in WRKY genes ranged from35.77~55.93 and 0.13~0.28,meaning the codon bias was weak and WRKY genes expression level was low.Bases composition analysis,neutral mapping analysis,ENC-plot analysis,and PR2-plot analysis indicated that the codon usage bias patterns in WRKY gene family were influenced by mutation and natural selection pressure.In addition,only one codon was determined for WRKY genes.All together,the results of this study provide important information for codon optimization on transgenic studies of tomato(Solanum lycopersicum)WRKY genes in the future.