‘波邦’咖啡叶绿体基因组密码子使用特征研究

Study on Codon Usage Characteristics in Chloroplast Genome of Coffea arabica'Bourbon'

本研究对小粒咖啡‘波邦’叶绿体基因组进行系统分析,探讨影响密码子使用偏性形成的因素。结果表明,‘波邦’叶绿体基因组密码子偏好性较弱,倾向于A/T结尾的密码子。ENC-GC3s绘图、PR2绘图以及中性绘图分析表明,‘波邦’密码子偏好性受突变影响的同时,也受自然选择等因素的影响,但自然选择起到更大的作用。进一步对应分析发现,基因表达水平、基因长度、GC含量对‘波邦’密码子偏性也有影响。密码子使用频率结果表明,拟南芥、烟草和酿酒酵母可考虑作为‘波邦’基因的表达受体系统,其中,烟草与酿酒酵母更为理想。研究表明,在‘波邦’中发现了GCT、TGT、GAT等20个高频密码子,确定了GCA、GCT、TGT等21个最优密码子。

A systematic analysis of the chloroplast genome of Coffea arabica'Bourbon',was conducted exploring the factors affecting the formation of codon usage bias.The results indicated that the codon usage bias in the chloroplast genome of'Bourbon'was weak,tending towards codons ending in A/T.The ENC-GC3s plot,PR2 plot,and neutral plot analysis indicated that the preference of'Bourbon'codons was influenced not only by mutations but also by factors such as selection,but natural selection played a greater role.Further correspondence analysis revealed that gene expression levels,gene length,and GC content also had an impact on the bias of the'Bourbon'codon.The results of codon usage frequency indicated that Arabidopsis thaliana,Nicotiana tabacum,and Saccharomyces cerevisiae could be considered as expression receptor systems for the'Bourbon'gene,but N.tabacum and S.cerevisiae being more ideal.Study showed that 20 high-frequency codons such as GCT,TGT,GAT,etc.were discovered in Bobon coffee,and 21 optimal codons such as GCA,GCT,and TGT were determined.