皱边喉毛花及其近缘物种的叶绿体基因组结构与进化分析

为重建喉毛花属下系统发育关系，明晰属下皱边喉毛花及其近缘种之间的物种关系。本研究利用Illumina高通量测序平台对12 个叶绿体基因组进行双末端测序，获得大量高质量的Clean reads用于后续生物信息学分析。结果表明：（1）喉毛花属下物种的基因组差异较小，均在150 kb左右，基因总数为131 个，其中编码基因81 个。IR区核苷酸多态性比SC低，编码区比非编码区更保守。（2）进化分析结果显示，几乎所有的编码基因受到纯化选择的作用。（3）密码子偏好性分析表明有35 个密码子的RSCU值均大于1，说明使用这些密码子的频率较高，各项密码子偏好性衡量指标说明喉毛花属物种的密码子偏好性较弱。（4）系统发育分析表明CDS、密码子位置与基因间隔区数据集构建的系统发育树具有高度一致的拓扑结构，大部分分支的支持率高。这些结果表明皱边喉毛花及其近缘种的叶绿体基因组无明显差异，在系统发育树上无法按物种聚类，也为后续展开喉毛花属下群体遗传学研究提供科学依据。

The Chloroplast Genome Structure and Evolution Analysis of Comastoma polycladum and Its Related Species

To reconstruct the phylogenetic relationship of the genus Comastoma and to clarify the species relationship for Comastoma polycladum and its related species. In this study, we sequenced the chloroplast genomes of 12 samples using the Illumina high-throughput sequencing platform, resulting in a large number of high-quality clean reads for subsequent bioinformatics analysis. The findings were as follows: (1) The distinction of chloroplast genome for the species of Comastoma was small, with the 150 kb of length, and we obtained a total of 131 genes, including 81 protein-coding genes (PCGs). The nucleotide polymorphisms in the IR region were lower than in the SC regions, and coding-protein regions were more conserved than non-coding regions. (2) The results of evolutionary analysis indicated that almost all PCGs may be subject to purifying selection. (3) Codon preference analysis revealed that the RSCU values of 35 codons were greater than one, indicating that these codons were used frequently, and codon preference measures revealed that the codon preference was weak. (4) Phylogenetic analysis revealed that the phylogenetic tree constructed using CDS, codon position, and intergenic spacer (IGS) regions datasets had a highly consistent topology, with most branches having a highly support. These results showed that there was no significant difference between the chloroplast genomes of Comastoma polycladum, and its related species, and that it was impossible to cluster them by species on the phylogenetic tree, which provided a scientific basis for future population genetic research on Comastoma.