'银辉'紫薇叶绿体基因组密码子偏好性分析
Codon Usage Bias of the Chloroplast Genome in Lagerstroemia indica'Ebony Glow'
李媚 1秦波 2刘玉军 1黄欣 2刘莉 1孙开道 2黄耀恒 2罗益敏1
作者信息
- 1. 广西壮族自治区南宁树木园,广西 南宁 530031
- 2. 广西壮族自治区林业科学研究院,广西林业实验室,广西特色经济林培育与利用重点实验室,广西 南宁 530002
- 折叠
摘要
为探究紫薇品种'银辉'叶绿体基因组特征、密码子使用模式及影响因素,采用高通量测序技术对'银辉'紫薇叶绿体基因组测序,筛选出 47 条蛋白质编码序列进行密码子偏好性分析.结果显示:'银辉'紫薇叶绿体基因组为典型的四分体结构,总长度为152 174 bp,GC含量为37.6%;基因组的有效密码子数(ENC)为35.73～61.00,密码子适应指数(CAI)为0.55～0.65,表明'银辉'紫薇叶绿体基因组密码子偏好性较弱;基因组的最优密码子有 11 个(AAU、ACA、AGA、AGU、CAU、CGA、CUU、GGA、UAU、UUG和UUU),表明'银辉'紫薇叶绿体基因组的密码子偏好以A或U结尾;中性绘图的回归系数为0.261 6,且有效密码子绘图显示实际ENC和理论ENC差异较大,表明自然选择是影响密码子偏好性的主要因素.
Abstract
This study aims to explore the characteristics as well as the codon usage pattern and influencing factors of the chloroplast genome in Lagerstroemia indica'Ebony Glow'.High-throughput sequencing was employed to sequence the genome of this plant.Forty-seven coding sequences were selected for the analysis of codon usage bias.The results revealed that the chloroplast genome of L.indica'Ebony Glow'exhibited a typical tetrad structure,with a total length of 152 174 bp and the average GC content of 37.6%.The effective number of codons(ENC)ranged from 35.73 to 61.00,and the codon adaptation index(CAI)ranged from 0.55 to 0.65,which indicated a weak preference for specific codons in the chloroplast genome of L.indica'Ebony Glow'.The genome contained 11 optimal codons(AAU,ACA,AGA,AGU,CAU,CGA,CUU,GGA,UAU,UUG,and UUU),which suggested a preference for ending with A/U.The neutral mapping demonstrated a linear regression slope of 0.261 6 and the ENC plotting showed a large difference between measured ENC and theoretical ENC,which suggested that natural selection was the primary factor influencing codon usage bias.
关键词
'银辉'紫薇/密码子偏好性/叶绿体基因组/最优密码子Key words
Lagerstroemia indica'Ebony Glow'/codon usage bias/chloroplast genome/optimal codon引用本文复制引用
出版年
2024
国家科技期刊平台
NSTL
万方数据