毛茛科和芍药科叶绿体基因组密码子特征和系统发育比较

为研究和比较毛茛科和芍药科叶绿体基因组密码子使用模式和系统进化关系，以完成测序的毛茛科33种植物、芍药科7种植物叶绿体基因组为材料，采用分析软件CodonW在线软件CUSP和R软件对叶绿体基因进行密码子特征分析。用MAFFT 软件，MEGA软件进行系统发育分析。研究结果表明芍药科植物叶绿体基因组和毛茛科植物（耧斗菜属除外）叶绿体基因组高频密码子一致性高，具有29个高频密码子，基本偏向与于A/U结尾，但最优密码子存在差异。毛茛科和芍药科叶绿体基因组密码子偏好性的形成因素主要受自然选择的影响，且芍药科叶绿体基因组密码子偏好性受自然选择的影响大于毛茛科。基于叶绿体基因组全序列和基于叶绿体基因组CDS序列的系统进化关系表明，芍药科基于叶绿体基因组全序列和基于叶绿体基因组CDS序列的系统进化关系虽然部分不同，但都可以被划分为芍药组和牡丹组。毛茛科基于叶绿体基因组的系统进化关系不符合中国植物志分类关系，但支持把毛茛科划分为4亚科14族。系统进化分析结果也支持芍药科独立于毛茛科和毛茛目，被划分到虎耳草目，同时证明了叶绿体基因组作为超级DNA条形码的可行性。

Comparison of Codon Characteristics and Phylogeny of Chloroplast Genome between Ranunculaceae and Paeoniaceae

To clarify the codon usage pattern and phylogenetic relationship of the chloroplast genome between Ranunculaceae and Paeoniaceae， 33 species of Ranunculaceae and seven species of Paeoniaceae were used as materials， and the analysis software CodonW， online software CUSP， and R software were used to analyze the codon characteristics of chloroplast genes， while the MAFFT software， MEGA software were used for phylogenetic analysis respectively. The results showed that the chloroplast genomes of Paeoniaceae and Ranunculaceae （except Columbine） had a high consistency of high frequency codons， with 29 high frequency codons， which were basically biased towards ending with A/U， but the optimal codon were different. The codon bias of the chloroplast genome of Ranunculaceae and Paeoniaceae was mainly influenced by natural selection， and the codon bias of the chloroplast genome of Paeoniaceae was more affected by natural selection than that of Ranunculaceae. The phylogenetic relationship based on the complete chloroplast genome sequence and the CDS sequence of the chloroplast genome showed that although the phylogenetic relationship based on the complete chloroplast genome sequence and the chloroplast genome CDS sequence of Paeoniaceae was different， they could be divided into the peony group and the peony group. The phylogenetic relationship of Ranunculaceae based on the entire chloroplast genome sequence did not conform to the classification relationship of Chinese flora， but it supported the division of Ranunculaceae into four subfamilies and 14 families. The analysis results supported that Paeoniaceae were independent from Ranunculaceae and Ranunculus， and were classified into Saxifraga.