摘要
通过分析灰毛浆果楝叶绿体基因组密码子的使用特征,探讨影响其密码子使用偏性的主要因素。从灰毛浆果楝叶绿体基因组中筛选出54条编码序列(CDS),利用Codon W 1.4.2和CUSP软件计算不同基因密码子各位置的GC含量,以明确灰毛浆果楝叶绿体基因组密码子的使用偏性规律。结果显示:灰毛浆果楝叶绿体基因组密码子第3位碱基的GC含量为28.95%,即第3位密码子富含A和U,有效密码子数(Nec)在34.60~61.00之间,Nec值大于45的CDS有39个;相对同义密码子使用度(URSC)值大于1的密码子有29个,其中16个以U结尾,12个以A结尾;中性绘图分析结果显示GC 12和GC 3的相关系数为0.0984,相关性不显著,回归系数(对角线斜率)为0.1379;基因N ec比值大多数分布在-0.05~0.05区间外,即大部分基因N ec值与预期值差距较大;相关关系分析显示,GC 3与GC1、GC2均未达到显著相关,Nec与GC3呈极显著相关。综合分析发现灰毛浆果楝叶绿体基因组密码子偏好性较弱,选择为主要影响因素,同时受到其他因素的影响。结合高表达优越密码子和高频密码子确定GUU、GUA、UCU、AGU、CCU、ACU、GGU、GCU、CAA、AAA、UGU、AGA和AUU等13个密码子为最优密码子。
Codon usage characterization of the Cipadessa cinerascens chloroplast genome was done to determine the factors influencing codon bias.Fifty-four coding DNA sequences were selected from the C.cineraseces chloroplast genome and the genes analyzed using Codon W 1.4.2 and CUSP.According to the results,the GC content at the 3rd codon position in the C.cineraseces chloroplast genome was 28.59%.In addition,the 3rd codon position was rich in A and T,and the N ec value was in the 34.60-61.00 range.Furthermore,there were 39 genes when the N ec value was higher than 45.Twenty-nine codons exhibited relative synonymous codon usage values greater than 1,including at the end with 16 U codons and 12 A codons.The neutrality plots revealed that the correlation coefficient of GC 12 and GC 3 was 0.0984,and that there was no significant correlation between GC 12 and GC 3.The regression coefficient(the diagonal line slope)was 0.1379 and the N ec ratios of most of the genes were beyond-0.05 to 0.05.The disparities between the actual N ec and the expected N ec values for the genes were very large.Although the correlation analysis revealed no significant correlation between GC 3 and GC 1,GC 2,there was an extremely high and significant correlation between N ec and GC 3.The codon usage bias in the C.cinerascens chloroplast genome was weak based on the comprehensive analysis performed,mainly due to the effect of selection,in addition to other factors.Furthermore,analysis of the high-expression codons and high-frequency codons verified 13 codons as the optimal codons,including GUU,GUA,UCU,AGU,CCU,ACU,GGU,GCU,CAA,AAA,UGU,AGA,and AUU.
作者
原晓龙
王毅
张劲峰
YUAN Xiaolong;WANG Yi;ZHANG Jingfeng(Yunnan Academy of Forestry and Grassland,Kunming,Yunnan 650201,China;Yunnan Key Laboratory of Forest Plant Cultivation and Utilization,Kunming,Yunnan 650201,China)
出处
《森林与环境学报》
CSCD
北大核心
2020年第2期195-202,共8页
Journal of Forest and Environment
基金
国家自然科学基金项目(31860177)
云南省林业和草原科学院热带亚热带珍贵用材树种研发创新课题(2017HC024)。
