4种霸王属植物叶绿体基因组密码子偏好性分析  

Analysis of codon preference in chloroplast genomes of four Zygophyllum species

作　　者：周美 王金涛 庄重 赵伟 张玲[1,2] ZHOU Mei;WANG Jintao;ZHUANG Zhong;ZHAO Wei;ZHANG Ling(College of Life Science and Technology,Tarim University,Alar,Xinjiang 843300,China;Xinjiang Produdion&Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin,Alar,Xinjiang 843300,China;Baotou Agricultural and Livestock Products Quality and Safety Center,Baotou,Inner Mongolia 014000,China)

机构地区：[1]塔里木大学生命科学与技术学院,新疆阿拉尔843300 [2]新疆生产建设兵团塔里木盆地生物资源保护利用重点实验室,新疆阿拉尔843300 [3]包头市农畜产品质量安全中心,内蒙古包头014000

出　　处：《西北植物学报》2024年第9期1445-1455,共11页Acta Botanica Boreali-Occidentalia Sinica

基　　金：国家自然科学基金项目(31660048)。

摘　　要：【目的】分析4种霸王属植物叶绿体基因组密码子的使用模式及其成因,为深入理解霸王属植物的密码子优化、偏好机制研究及遗传进化关系提供科学依据。【方法】用CodonW、EMBOSS等对叶绿体基因组筛选出的40条基因编码序列密码子进行ENC-plot、中性绘图、最优密码子等分析。【结果】4种霸王属植物叶绿体基因组密码子的GC含量依次为GC_(1)>GC_(2)>GC_(3),ENC平均值都大于35,CAI均为0.17,其基因表达水平较低,且密码子使用偏好性较弱;中性绘图分析、ENC-plot及PR2-plot分析认为4个物种叶绿体基因组密码子的偏好性主要受自然选择作用的影响;最优密码子分析表明豆型霸王、长梗霸王、霸王和喀什霸王最优密码子分别有19,13,14,14个,其中4个为共有密码子且以A/U收尾。【结论】4种霸王属植物的密码子碱基多以A/U结尾,偏好性较弱且主要影响因素为自然选择,鉴定出CGA、GAA、UAU、UUA这4个共有最优密码子。[Objective]Codon usage bias of four Zygophyllum chloroplast genomes,and their main patterns and causes were analyzed for better understanding of the codon optimization,preference mechanism,and genetic evolution relationship of Zygophyllum.[Methods]The parity preference(PR2-plot)analysis,effective number of codons(NEC-plot),neutrality plot,and RSCU cluster analysis of 40 genes from four Zygophyllum species were carried out using CodonW,EMBOSS,and other softwares in this study.[Results]The codon usage patterns in the plastomes of four Zygophyllum species were similar,the GC content of codon was followed by GC_(1)>GC_(2)>GC_(3),the average ENC values were more than 35,and the CAI was 0.17,indicating that gene expression of the chloroplast genome of Zygophyllum species was low and codon preference was weak.The results of neutral mapping analysis,ENC-plot selection,and PR2-plot analysis showed that the codon usage pattern was predominantly affected by natural selection.RSCU cluster analysis showed that Z.fabago,Z.obliquum,Z.xanthoxylum,and Z.kaschgaricum had 19,13,14,and 14 optimal codons,respectively.By constructing the high and low gene expression library of the target genes,four optimal genes were selected that were ending with A/U.[Conclusion]Codon bases of the chloroplast genome from four Zygophyllum species are mostly ended with A/U.The preference is weak and the main influencing factor is natural selection.Four optimal codons,including CGA,GAA,UAU and UUA,are identified in this study.

关 键 词：霸王属 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：Q755[生物学—分子生物学] S567.1[农业科学—中草药栽培]