滇南青冈叶绿体基因组特征及密码子使用偏好性分析

Chloroplast genome characteristics and codon usage bias analysis of Quercus austroglauca Y.T.Chang

为了明确滇南青冈(Quercus austroglauca Y.T.Chang)叶绿体基因组的结构特征、密码子使用偏好性及其影响因素,本研究运用Geneious、CodonW等软件,对其进行了系统分析。结果显示,滇南青冈的叶绿体基因组全长160913 bp,编码133个基因。从中筛选出的52条蛋白编码序列第3位碱基的平均GC含量为29.14%,说明其密码子偏爱以A或U结尾,相对同义密码子使用度分析结果也印证了这一点。有效密码子数(ENC)均大于35,表明其密码子偏好性较弱。中性绘图分析、ENC-plot分析以及PR2-plot分析结果均表明,影响滇南青冈叶绿体基因组密码子使用偏好性的主导因素是自然选择。通过筛选确定,其最优密码子共有13个。多重分析结果显示,变异多在非编码区域,编码区ycf1基因的变异程度较大。IR边界分析显示滇南青冈存在ycf1假基因。系统发育分析表明滇南青冈与多脉青冈(Q.hypargyrea(Seemen)C.C.Huang et Y.T.Chang)等栎属植物亲缘关系较近。

In this study,we sequenced the chloroplast genome of Quercus austroglauca Y.T.Chang and analyzed the structural characteristics of the chloroplast genome and factors influencing codon preference using various software.Results showed that the chloroplast genome of Q.austroglauca was 160913 bp in length,encoding 133 genes.Analysis of 52 screened protein-coding sequences revealed an average GC content of the third base of 29.14%,signifying a pronounced preference for A or U as the terminal codon.These results were confirmed by relative synonymous codon usage analysis.Number of effective codons(ENC)was greater than 35,indicating weak codon preference.Neutral mapping,ENC-plot,and PR2-plot analyses showed that natural selection was the dominant factor affecting codon preference in the Q.austroglauca chloroplast genome.In total,13 optimal codons were identified by screening.Multiple analysis showed that variation mostly occurred in the non-coding regions,although the ycf1 gene exhibited a large degree of variation in the coding region.Inverted repeat(IR)boundary analysis identified a ycf1 pseudogene in Q.austroglauca Phylo-genetic analysis showed that Q.austroglauca was closely related to Q.hypargyrea(Seemen)C.C.Huang et Y.T.Chang.