芒果叶绿体基因组密码子使用偏好性分析

本研究利用CodonW、SPSS、Excel软件对芒果叶绿体基因组55条蛋白编码序列的密码子开展了中性绘图、PR2-plot、ENC-plot和最优密码子分析。结果表明,芒果叶绿体基因的有效密码子（ENC）偏好性不强,分布在35.38~56.56;GC3s含量26.29%,说明密码子末位碱基以A/T结尾为主;ENC与GC3极显著相关。相对同义密码子分析,RSCU>1的密码子有31个,其中,以A和T结尾的29个,表明A和T是基因组偏爱的密码子。中性绘图、PR2-plot和ENC-plot分析表明,芒果叶绿体基因组密码子使用偏好受突变和选择等因素共同作用的影响。通过高频率密码子和高表达优越密码子相结合的方法进行分析,筛选出主要以A和T结尾的芒果叶绿体基因组最优密码子19个,分别是GCT、TGT、GAA、TTT、GGT、CAT、ATT、AAA、TTA、CCT、CAA、AGA、CGA、CGT、AGT、TCT、ACT、GTA 和CTT。

Analysis on Codon Usage Bias of Chloroplast Genes from Mango

Codon usages of 55 chloroplast genes in mango were analyzed to obtain to the results of neutrality plot, PR2-plot ENC-plot and optimal codons by using CodoW, SPSS and SPSS softwares. The results showed that the effective number of codons (ENC) ranged from 35.38 to 56.56, indicating that the condon bias was weak. GC base pair content in the third condon position of chloroplast genomes in mango was 26.29%, indicating that the third base in the codon was terminated by A/T. Significant correlation was found between ENC and GC3.There were 31 codons with relative synonymous codon usage greater than 1, of which 29 codons ending with A and T, indicating that the third codon preferred A and T.According to neutrality plot analysis, PR2-plot and ENC-plot analysis, mutational pressure combined with selection influenced the pattern of synonymous codon usage across genes in mango chloroplast genomes. In addition 19 codons were affirmed as the optimal codons by using analysis of high-frequency codons and the high expression codons, ending with A and T. There were GCT, TGT, GAA, TTT, GGT, CAT, ATT, AAA, TTA, CCT, CAA, AGA, CGA, CGT, AGT, TCT, ACT, GTA and CTT.