永椿香槐叶绿体基因组密码子偏好性分析

Analysis on Codon Usage Bias of Chloroplast Genome in Cladrastis yunchunii X.W.Li&G.S.Fan

为分析永椿香槐叶绿体基因组密码子偏好性使用模式,以永椿香槐叶绿体基因组中的40条蛋白质编码序列为研究对象,利用Codon W 1.4.2和CUSP在线软件对永椿香槐叶绿体基因组进行了中性绘图分析、ENC-plot和PR2-plot分析。结果表明,永椿香槐叶绿体基因组密码子不同位置上的GC含量依次是GC_(1)(46.33%)>GC_(2)(39.81%)>GC_(3)(29.58%),表明叶绿体基因组密码子末位碱基偏好以A和U结尾;其ENC的范围为34.93~55.78,有27个ENC值>45,表明其密码子的偏好性较弱;RSCU>1的密码子中有29个以A、U结尾。中性分析显示,GC_(12)和GC_(3)的相关系数和回归系数分别为0.126 0和0.224 3,相关性不显著;ENC-plot分析显示ENC频数比值在-0.05~0.05间的有12个,这部分基因密码子偏好性主要受选择的影响;PR2-plot分析中,T>A、G>C,说明永椿香槐叶绿体基因组密码子偏好性受多种因素影响;15个密码子确定为最优密码子,如UUU、UUA、AUU等。综上所述,永椿香槐叶绿体基因组密码子的使用主要受选择的影响,研究结果可为永椿香槐叶绿体基因工程、种源鉴定提供科学依据。

tIn order to analyze the codon usage patterns of the chloroplast genomes of Cladrastis yunchuni,40 CDS of C.yunchunii chloroplast genome were used as the research object,and the codons were analyzed by neutral plotting,ENC-plot and PR2-plot using Codon W 1.4.2 and online software CUSP.The results showed that the GC content at different positions of the codons in the chloroplast genome of the locust locust is GC_(1)(46.33%)>GC_(2)(39.81%)>GC_(3)(29.58%).Indicating that the chloroplast genome codon last base preference is A and U end;the chloroplast genome ENC range is 34.93~55.78,and there are 27 ENC values>45,indicating that its codon preference is weak;there were 29 codons of RSCU>1 in the end of A,and U;neutral drawing analysis shows that the correlation coefficients and regression coefficients of GC_(12) and GC_(3)are 0.1260 and 0.2243,respectively,and the relevance is not significant;ENC-plot analysis shows that there are 12 ENC frequency ratios between-0.05~0.05,and the codon preference of these genes is mainly affected by choice;PR2-Plot analysis,T>A,G>C;it showed that the codon preference of the chloroplast genome of C.yunchuni is affected by many factors;15 codons such as UUU,UUA,AUU,etc.To sum up,the use of codons in the chloroplast genome of C.yunchuni is mainly affected by selection.The results of the study can be a scientific basis for C.yunchuni chloroplast genetic engineering and its provenance identification.