湖北山楂叶绿体基因组密码子偏好性分析

Analysis of Codon Bias in the Chloroplast Genome of Cratae gus hupehensis Sarg.(Rosaceae)

为探究湖北山楂叶绿体基因组密码子的偏好性及偏好性的成因,本研究以湖北山楂叶绿体基因组中的53条CDS为研究对象,具体使用了Codon W 1.4.2和在线软件CUSP进行ENC-plot、PR2-plot和中性绘图等进行分析。结果表明,湖北山楂叶绿体基因组中密码子GC含量为GC_(1)(46.99%)>GC_(2)(39.45%)>GC_(3)(28.37%),有效密码子数(ENC)值大于45的有40个。相对同义密码子使用度(RSCU)分析结果表明,有32个密码子的RSCU>1,其中以A和U结尾的有29个,说明湖北山楂叶绿体基因组A/U使用的频率较高。中性绘图分析发现,GC_(3)与GC_(1)、GC_(2)的相关性不显著,说明密码子偏好性的成因主要是受选择因素的影响。通过中性绘图分析、ENC-plot分析和PR2-plot分析得到主要结论:选择作为主要因素影响着湖北山楂叶绿体基因组密码子的偏好性。此外,通过构建的高低基因表达库最终确定12个最优密码子:UAG、UUC、GUA、UUA、GUU、UCU、CCU、CAA、AAA、AUU、GAA和CGA。本研究揭示了影响密码子偏好性形成的主要因素,为基因工程理论研究和目标性状的改良奠定了科学基础。

To determine the codon usage pattern of the chloroplast genome of Crataegus hupehensis Sarg.(Rosaceae),53 protein-coding sequences were screened out in the chloroplast genome of C.hupehensis Sarg.(Rosaceae).CodonW 1.4.2 and online software CUSP was used to analyze their codon preference.The results demonstrated that the GC content of the codons in the chloroplast genome of C.hupehensis Sarg.(Rosaceae)is GC_(1)(46.99%)>GC_(2)(39.45%)>GC_(3)(28.37%).There were 40 effective codon numbers(ENC)values greater than 45,which indicated that the chloroplast genome bias of C.hupehensis Sarg.(Rosaceae)was weak.The relative synonymous codon usage(RSCU)analysis showed that there were 32 codon numbers in RSCU>1,of which 29 codon numbers ended in A and U,which indicated that A or U appeared more frequently in the chloroplast genome of C.hupehensis Sarg.(Rosaceae).Neutral instruction showed that GC_(3),is relevant to GC_(1),GC_(2) was not significant,indicating that the codon bias was mainly affected by natural selection.ENC-plot analysis showed that some genes fell below and around the curve,suggesting that mutations also influenced the formation of partial codon bias.In addition,12 optimal codons,UAG,UUC,GUA,UUA,GUU,UCU,CCU,CAA,AAA,AUU,GAA and CGA,were determined by constructing the high and low gene expression library.This study reveals the main factors affecting the formation of codon preference and provides a reference for genetic engineering research and improvement of target traits.