大山樱叶绿体基因组特征及密码子偏好性分析

Analysis of Codon Usage Bias in the Chloroplast Genome of Prunus sargentii

为了明确大山樱叶绿体基因组特征及其密码子使用偏好,共筛选53条叶绿体CDS基因序列作为分析对象。使用CodonW 1.4.4等软件对大山樱密码子使用偏好性进行分析。结果表明,大山樱叶绿体基因组GC3含量为28.84%,含量较低;RECU>1的30个密码子中,有29个以A/U结尾;ENC平均值为47.54,证明其密码子偏好性较弱。3种绘图分析结果均表明自然选择对密码子偏好性影响较大。最终确定10个最优密码子,且7个以A/U结尾。基于CDS序列和RSCU值的系统发育分析及聚类分析结果相似,表明密码子偏好性和物种系统发育关系有一定关联。该结果为研究樱亚属植物叶绿体基因组特征及其密码子偏好性提供了相关依据。

To determine the codon usage pattern of chloroplast genome and analyzed the genome sequencing structure of Prunus sargentii. 53 protein coding sequences in the chloroplast genome were analyzed by CodonW1.4.4. The results showed that the chloroplast genome GC_3 content of Prunus sargentii was 28.84%, which was relatively low;of the 30 codons of RECU >1, 29 end in A/U;the average effective number of codons was 47.54,which indicates that their codon usage bias was weaker. These three kinds of graphical analysis showed that the main factor affecting the codon preference was natural selection. 10 codons to be affirmed as the optimal codon,seven of these codons end with A/U. The consistencies between the result of clustering analysis based on RSCU and the NJ-tree based on CDS suggest that the codon preference is related to the phylogenetic relationship among species. This study reveals the main factors affecting Prunus sargentii the codon preference, and provides a basis for genetic relationship study of the Prunus subg. cerasus.