不同作物FAD2基因密码子偏好性分析

Analysis of Codon Usage Bias of FAD2 Gene in Different Crops

本研究运用多种软件对12种作物的FAD2基因进行密码子偏好性分析。结果表明:FAD2基因在12种作物中密码子使用偏好性差异很大,禾本科作物玉米、水稻、高粱的FAD2基因有效密码子数(Effec-tive Number of Codons,ENC)在30左右,为偏好性很强的基因;油料作物油菜和亚麻的FAD2基因的ENC值分别为45.49和48.58,为一般偏好性基因;另外6种油料作物和模式植物拟南芥的FAD2基因ENC值都大于50,偏好性较弱。玉米、水稻、高粱、油菜、亚麻、花生和拟南芥的FAD2基因偏好以G或C碱基结尾的密码子,其余5种油料作物的FAD2基因偏好使用以A或T结尾的密码子。在12种作物中,密码子CTC的RSCU值都大于1,属于高频使用的密码子;而CTA、ATA、GTA、AGT、CCC属于低频密码子。在聚类分析中,12种作物基于FAD2基因密码子用法与基于CDS序列的聚类结果大体一致。

In this study,the codon usage bias of fatty acid desaturase gene,FAD2,from 12 crop species was analyzed by several softwares.The results showed that there were great differences in codon usage bias of FAD2 gene in different crops.The effective number of codons（ENC） of FAD2 genes in gramineous crops,such as Zea mays,Oryza sativa and Sorghum bicolor,was about 30,which indicated these genes were highly biased;FAD2 genes in oil crops,Ricinus communis and Linum usitatissimum,were moderately biased with ENC as 45.49 and 48.58 respectively;FAD2 genes in other 6 oil crops and Arabidopsis thaliana were low biased with ENC more than 50.FAD2 genes in Zea mays,Oryza sativa,Sorghum bicolor,Brassica napus,Linum usitatissimum,Arachis hypogaea and Arabidopsis thaliana preferred to use condons ended with G or C,those genes in other 5 oil crops preferred to use codons ended with A or T.In 12 crop species,CTC was highly frequently used codon with RSCU value more than 1;CTA,ATA,GTA,AGT,CCC were rarely used codons.Clustering results of 12 crop species based on the codon usage and CDS sequence of FAD2 gene were nearly consistent.