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GC1＞GC2＞GC3,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.
Abstract
[Objective]Codon usage bias of four Zygophyllum chloroplast genomes,and their main pat-terns 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 GC1＞GC2＞GC3,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.
维普
万方数据