蚕豆细胞器基因组密码子的使用情况分析

Aanlysis of usage of codons in organelle genomes of Vicia faba L.

为了揭示蚕豆细胞器基因组密码子的使用模式,利用Codon W 1.4.2和CUSP软件分别对蚕豆线粒体和叶绿体基因组的编码序列进行中性绘图、ENC-plot分析、PR2-plot分析以及密码子偏好性的影响因素分析,从中得到最优密码子.结果显示:蚕豆线粒体和叶绿体基因组的平均GC含量分别为46.48%和37.16%,密码子第3位碱基的平均GC含量分别为45.43%和27.10%;有效密码子数的范围分别为40.40~61.00和38.11~51.65,平均值分别为53.75和45.06;线粒体和叶绿体基因组中RSCU>1的密码子各有29个和30个,其中以A/U结尾的各有23个和29个,以C/G结尾的各有6个和1个.中性绘图分析显示,线粒体和叶绿体GC_(12)与GC_(3)之间的相关系数分别为0.374和0.145,相关性不具有统计学意义(P>0.05),回归系数分别为0.255和0.327;ENC-plot分析显示,大部分基因与标准曲线的距离较远;PR2-plot分析显示,碱基在使用频率方面U>A、G>C,说明蚕豆细胞器基因组密码子的偏好形成主要受到自然选择的影响.有39个密码子既满足高频率也满足高表达的条件,属于最优密码子,仅有1个GUA是线粒体和叶绿体共有的最优密码子.同线粒体基因组相比,蚕豆中叶绿体基因组比线粒体基因组更易受到自然选择的影响.

In order to explore the codon usage pattern of organelle genome in Vicia faba L.,Codon W 1.4.2 and CUSP software were used to analyze the coding sequences of the mitochondrial and chloroplast genomes of V.faba by neutral mapping,ENC-plot and PR2-plot analysis,as well as the influencing factors of codon preference,from which the optimal codon was obtained.The results showed that the average GC content of the mitochondrial and chloroplast genomes of V.faba was 46.48%and 37.16%,respectively,and the average GC content of the third codon base was 45.43%and 27.10%,respectively.The effective codon numbers ranged from 40.40 to 61.00 and 38.11 to 51.65,with mean values of 53.75 and 45.06,respectively.There were 29 and 30 codons with RSCU>1,among which 23 and 29 codons had A/U endings,and six and one codon had C/G endings,respectively,in mitochondrial and chloroplast genomes.Neutral mapping analysis showed that the correlation coefficient between GC_(12)and GC_(3)was 0.374 in chloroplast,and was 0.145 in mitochondrion,and the regression coefficient was 0.255 in chloroplast and 0.327 in mitochondrion.The ENC-plot analysis showed that most genes were far away from the standard curve.PR2-plot analysis showed that the base use frequency was U>A and G>C,indicating that the codon preference formation of organelle genome in V.faba was mainly influenced by selection among various factors.Thirty-nine codons met the conditions of high frequency and high expression,and only one GUA was the optimal codon shared by mitochondrion and chloroplast.It was found that chloroplast genome was more susceptible to natural selection than mitochondrial genome.