小粒咖啡铁皮卡叶绿体基因组密码子偏好性分析

Codon Usage Bias of the Chloroplast Genome in Coffea arabica'Typica'

为了解铁皮卡叶绿体基因组密码子的使用特征及其成因,以筛选的52条蛋白编码序列为研究对象,利用CodonW和CUSP在线软件对其密码子使用特征进行系统分析。结果表明,基因组各位置的GC含量GC 1、GC 2、GC 3分别为47.47%、39.52%、27.92%,30个高频密码子中,以U结尾占比53.33%,以A结尾占比43.33%,以G结尾占比3.33%,说明铁皮卡叶绿体基因偏好使用NNA和NNU型密码子,尤其偏好使用NNU型密码子。有效密码子数(ENC)、密码子适应指数(CAI)、最优密码子频率(Fop)分别为46.85、0.167、0.352,均揭示该基因组的密码子偏性较弱。中性绘图、ENC-plot、PR2-plot以及对应分析揭示密码子的偏好性受到选择及其他因素共同作用,最终确定了AUU、GUU和UCU等20个最优密码子。表明铁皮卡叶绿体基因组密码子的偏性较弱,偏好AU结尾的密码子。密码子的使用偏好性受到突变及选择等多种作用共同影响。

To dissect the codon usage bias of the chloroplast genome codons and contributing factors,52 protein coding gene sequences from the chloroplast genome of Coffea arabica'Typica'were studied.CodonW and CUSP online software were used to analyze the characteristics of its codon usage.It was found out that the GC 1,GC 2 and GC 3 contents were 47.47%,39.52%and 27.92%,respectively,among the 30 high-frequency codons,53.33%ended with U,43.33%ended with A,and 3.33%ended with G,indicating that the chloroplast genes of C.arabica'Typica'preferred to NNA and NNU codons,especially NNU codons.The effective codon number(ECN),codon adaptation index(CAI)and optimal codon frequency(Fop)were 46.85,0.167 and 0.352,respectively,suggesting that the codon bias of the genome was weak.The Neutral plot analysis,ENC-plot analysis,PR2-plot analysis and correspondence analysis showed that codon usage bias was influenced by selection and other factors.Finally,20 codons,including AUU,GUU and UCU,were identified as the optimal codons.In summary,the codon usage bias of C.arabica'Typica'is weak,and prefers to the AU ending codons.Multiple factors contribute to the codon usage bias,such as selection and mutation.