香花油茶叶绿体基因组密码子偏好性分析

Analysis on codon usage bias of the chloroplast genome of Camellia osmantha

【目的】为了分析香花油茶叶绿体基因组密码子偏好性,以筛选到的53条基因编码序列为研究对象,进行密码子组成成分和偏好性分析,进而找出香花油茶叶绿体基因组最优密码子,为该物种基因组研究及其遗传改良提供理论基础。【方法】利用Codon W 1.4.2、在线软件CUSP及Python3.7对香花油茶叶绿体基因组序列进行中性绘图、ENC-plot和PR2-plot绘图分析,探究影响密码子偏好性的主要因素,并通过ΔRSCU法预测最优密码子。【结果】1)香花油茶叶绿体基因组中,RSCU>1的密码子数目为31个,其中以U结尾的有16个,以A结尾的有12个,以G结尾的有3个;2)密码子三碱基中的平均GC_all含量为37.85%,且GC1(45.87%)>GC2(39.67)>GC3(28.03%);3)ENC-plot分析发现,ENC值位于24.1~61.0之间,平均值为40.09,香花油茶的ENC范围明显大于普通油茶(35.23~56.67);4)相关性分析发现,GC12与GC3相关性不显著,此外密码子第三个碱基上U的使用频率高于A,G的使用频率高于C;5)通过ΔRSCU值法,找出香花油茶叶绿体基因组中5个最优密码子,分别为GAU、GGU、UUG、CCU、AGA。【结论】香花油茶叶绿体基因组密码子碱基多以A或U结尾。该物种叶绿体基因组中密码子偏好性不仅受碱基突变影响,自然选择也发挥着不可替代的作用。鉴定出5个最优密码子,存在较少最优密码子的原因可能是由于该物种在进化过程中受到纯化选择的压力。

【Objective】In order to analyze the codon usage bias of the chloroplast genome of Camellia osmantha,the study analyzed the codon composition and codon usage bias of 53 selected gene-coding sequences and identified the optimal codons to provide a theoretical basis for the genome research and genetic improvement of C.osmantha.【Method】Codon W 1.4.2,the online software CUSP and Python 3.7 were used to analyze the neutrality plots,ENC-plot and PR2-plot of C.osmantha chloroplast genome sequences,to explore major factors influencing codon usage bias and predict the optimal codons by usingΔRSCU method.【Result】1)The number of codons with RSCU>1 was 31,of which 16 ended with U,12 ended with A and 3 ended with G.2)The average GC content in three bases was 37.85%,and GC1(45.87%)>GC2(39.67)>GC3(28.03%).3)ENC-plot analysis revealed that the ENC values were between 24.1 and 61.0,with a mean value of 40.09,and the ENC range of C.osmantha was significantly larger than that of Camellia oleifera(35.23-56.67);4)Correlation analysis revealed that GC12 was not significantly correlated with GC3.The usage frequency of U was higher than that of A,and the usage frequency of G was higher than that of C in the third codon position,which indicated that the third codon base was biased.5)We have identified the five optimal codons of C.osmantha chloroplast genome,which were GAU,GGU,UUG,CCU and AGA.【Conclusion】The codon bases of C.osmantha chloroplast genome mostly ended with A or U.The codon usage bias of C.osmantha chloroplast genome is not only influenced by base mutations but also by natural selection.Five optimal codons were identified in this study,and the presence of few optimal codons may be due to the evolutionary pressure of purifying selection in this species.