甘蓝S-位点基因SRK、SLG和SP11/SCR密码子偏好性分析  

Codon usage bias analysis of S-locus genes SRK,SLG,and SP11/SCR in Brassica oleracea

作　　者：张以忠 曾文艺 邓琳琼 张贺翠[1] 刘倩莹 左同鸿 谢琴琴 胡燈科 袁崇墨 廉小平[1] 朱利泉[1] ZHANG Yi-Zhong;ZENG Wen-Yi;DENG Lin-Qiong;ZHANG He-Cui;LIU Qian-Ying;ZUO Tong-Hong;XIE Qin-Qin;HU Deng-Ke;YUAN Chong-Mo;LIAN Xiao-Ping;ZHU Li-Quan(College of Agronomy and Biotechnology,Southwest University,Chongqing 400715,China;Ecological Engineering School,Guizhou University of Engineering Science,Bijie 551700,Guizhou,China)

机构地区：[1]西南大学农学与生物科技学院,重庆400715 [2]贵州工程应用技术学院生态工程学院,贵州毕节551700

出　　处：《作物学报》2022年第5期1152-1168,共17页Acta Agronomica Sinica

基　　金：国家自然科学基金项目(31572127);中央高校基本科研业务费专项资金(XDJK2020D024)资助。

摘　　要：S位点是芸薹属植物自交不亲和反应的关键位点,控制自交不亲和反应的识别与启动。为明确甘蓝S位点基因SRK和SLG的S域和SP11/SCR编码序列密码子的使用特性,利用Codon W、SPSS软件、Python程序和EMBOSS在线程序分析甘蓝41个SRK、36个SLG和11个SP11/SCR等位基因的偏好性,同时通过中性绘图、ENC-GC3绘图、PR2绘图及多元统计分析探讨基因密码子偏好性形成原因,并利用不同方法对其进行聚类分析。结果表明,甘蓝SRK、SLG和SP11/SCR基因编码序列富含A/T,密码子偏好以A/T碱基结尾,偏好性较低。自然选择是影响密码子使用模式的主要因素,突变压力为次要因素,还受到二核苷酸丰度的影响。根据RSCU值发现,SRK和SLG基因高表现密码子有4个,SP11/SCR基因有11个。基于RSCU的聚类能够较准确地反应甘蓝SRK、SLG和SP11/SCR等位基因间的关系,并与基于CDS核酸序列的聚类具有一致性和可靠性。根据密码子使用偏好性和聚类关系发现,SRK的S域和SP11/SCR编码序列在密码子偏好性上可能是协同进化的。这为更好理解甘蓝中密码子的分布机制和SRK、SLG和SP11/SCR基因的进化提供新内容。S-locus is the key locus in Brassica that controls the recognition and initiation of the self-incompatibility response.To clarify the codon usage characteristics of the S domain of S-locus genes SRK and SLG as well as of SP11/SCR coding sequence in Brassica oleracea,the codon usage bias of 41,36,and 11 alleles of SRK,SLG,and SP11/SCR were analyzed by Codon W,SPSS,Python,and EMBOSS online tools,respectively.Neutrality,ENC-GC3,and Parity Rule 2(PR2)plotting together with multivari-ate statistical analysis were also used for the exploration of possible factors that might affect the formation of the codon usage bias of these genes.The cluster analysis performed using various methods showed that S domains of SRK,SLG,and SP11/SCR genes of Brassica oleracea were rich in AT base pairs,the codon preference ended with A/T base and had a lower codon usage bias,which were affected by the natural selection(a main factor)and the mutational pressure(a secondary factor)as well as dinucleotide abundance.Based on the RSCU values,4 over-expressed codons of SRK and SLG,and 11 over-expressed codons of SP11/SCR were identified.Cluster analysis based on RSCU could accurately reflect the relationship among SRK,SLG,and SP11/SCR alleles in Brassica oleracea,which was consistent and reliable with CDS sequence clustering.According to codon us-age bias and cluster relationship,the S domain of SRK and the SP11/SCR coding sequence might be coevolutionary in the codon usage bias.This study enhances our understanding of the mechanism of distribution of codons and the evolution of SRK,SLG,and SP11/SCR genes in Brasscia oleracea.

关 键 词：甘蓝 自交不亲和 S-位点基因 密码子使用偏好 聚类分析 

分 类 号：S635[农业科学—蔬菜学]