基于叶绿体基因组解析半枫荷系统位置和进化

Plastid phylogenomics resolving phylogeny and evolution of Semiliquidambar cathayensis

关键词:  半枫荷, 蕈树科, 叶绿体基因组, 系统发育, 适应性进化

Key words:  Semiliquidambar cathayensis, Altingiaceae, chloroplast genome, phylogeny, adaptive evolution

摘要:

为明确国家二级保护植物半枫荷与近缘类群的系统发育关系,分析叶绿体基因的适应性进化。该研究利用22个物种的24条叶绿体基因组序列构建最大似然树和贝叶斯树,探讨半枫荷及其近缘类群的系统发育关系,并通过不同模型检测半枫荷与近缘类群的叶绿体编码基因的变异位点与选择压力间的关系。结果表明:(1)半枫荷叶绿体基因组具有133个基因,包括蛋白质编码基因88个(其中11个具有内含子)、tRNA基因37个、rRNA基因8个。(2)半枫荷及其近缘属蕈树属、枫香树属8个物种的叶绿体基因组在序列长度、基因数量及组成、GC含量等方面相对保守,反向重复区与小单拷贝区边界高度保守。小单拷贝区和大单拷贝区的变异程度较高,而反向重复区的变异程度较低。(3)半枫荷与蕈树属、枫香树属物种聚成蕈树科分支,并可划分为3个亚分支,亚分支间或物种间可能存在杂交或不完全谱系分选。(4)适应性进化结果显示,在不同模型下蕈树科分支的物种在ndhA等叶绿体基因受选择约束(纯化选择),位点模型也检测到10个基因的28个位点P大于0.99,这些编码基因变异可能与蕈树科植物适应性分化有关。该研究结果支持半枫荷隶属于蕈树科,蕈树科内物种的叶绿体基因可能存在适应性进化,这为同名异物类药材的资源保护和民族药的创新研发提供了参考资料。

Abstract:

Semiliquidambar cathayensis is treated as a grade-two protected plant in China. However, its phylogenetic relationships with species from Hamamelidaceae and Altingiaceae remain unclear. In order to analyze the phylogenetic relationships and adaptive evolution of chloroplast genomes between S. cathayensis and its closely related taxa including species from Hamamelidaceae and Altingiaceae, we reconstructed the maximum likelihood tree and the Bayesian tree to discover the phylogenetic relationships between S. cathayensis and its closely related taxa from 24 sequences that representing 22 species, and further detected the correlation between adaptive sites and selective pressure of protein coding genes under varying models including site model, clade model and branch model. Altingiaceae clade was chosen as the foreground clade. The results were as follows:(1)A total of 133 genes were annotated, including 88 protein-coding genes(11 genes with intron), 37 tRNA genes and eight rRNA genes.(2)Eight chloroplast genomes representing eight species from S. cathayensis and Altingia, Liquidambar were relatively conservative in sequence length, gene number and composition, GC content, and there was not obvious diversity in the four boundaries. Relatively high variation interspecific were also detected in LSC and SSC regions among these eight chloroplast genomes, while the IR regions were high conservatism.(3)Phylogenetic trees showed that S. cathayensis and sampled species of Altingiaceae clustered a group, which further divided into three clades, namely Clade I, Clade Ⅱ and Clade Ⅲ. The phylogenetic relationships among these clades remain unclear due to hybridization or incomplete lineage sorting(ILS)according to the results of test of ILS.(4)The chloroplast genes such as ndhA, ndhG and rps12 were subjected to selection pressure under the clade model and branch model. Furthermore, 28 sites of ten genes were detected under positive selection with P-value greater than 0.99 based on the site model, which may be related to the adaptive evolution of Altingiaceae. In this study, the results of plastid phylogenomics supports that S. cathayensis belongs to Altingiaceae. Several coding genes among these species of Altingiaceae may have adaptive evolution. These results will provide data for the further resource protection of homonym drugs and pharmacognostic researches of ethnodrug.