Zhou Sheng-Mao, Wang Fang, Yan Si-Yuan, Zhu Zhang-Ming, Gao Xin-Fen, Zhao Xue-Li
Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China.
School of Ecology and Environmental Science and Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China.
Front Plant Sci. 2023 Jun 6;14:1186598. doi: 10.3389/fpls.2023.1186598. eCollection 2023.
L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of .
Here, we newly assembled 18 chloroplast genomes of . We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.
The chloroplast genomes of exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which K-L, F-L, and 1 were considered as candidate DNA barcodes for species identification of . Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of and allied species. monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of suggested that species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in . These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus .
木蓝属是豆科的第三大属，包含具有重要经济价值的物种，可用于生产靛蓝染料、药用、观赏以及水土保持。由于种间形态特征高度重叠、分类的可靠状态较少以及广泛的适应性进化，该属在分类学上存在困难。先前基于特征的分类学和基于核ITS的系统发育研究有助于我们对分类学和进化的理解。然而，叶绿体基因组资源的缺乏限制了我们对木蓝属系统发育关系和进化过程的全面理解。
在此，我们新组装了18个木蓝属的叶绿体基因组。我们结合蝶形花亚科的近缘物种，对基因组结构、核苷酸多样性、系统发育分析、物种间Ka/Ks比率以及正选择分析进行了一系列研究。
木蓝属的叶绿体基因组结构高度保守，大小在157,918至160,040 bp之间，包含83个蛋白质编码基因、37个tRNA基因和8个rRNA基因。鉴定出13个高度可变区域，其中K-L、F-L和1被认为是木蓝属物种鉴定的候选DNA条形码。基于完整叶绿体基因组和蛋白质编码基因（PCG），使用最大似然法（ML）和贝叶斯推断法（BI）进行的系统发育分析产生了一个解析良好的木蓝属及其近缘物种的系统发育树。木蓝属的单系性得到了有力支持，并且在该属内解析出四个单系谱系（即泛热带、东亚、特提斯和古热带分支）。物种间Ka/Ks比率显示值低于1，并且在使用分支位点模型的正选择分析中鉴定出13个密码子位点后验概率显著的基因，其中8个与光合作用相关。木蓝属的正选择表明该属物种经历了对食草动物和病原体施加的选择压力的适应性进化。我们的研究为木蓝属叶绿体基因组的结构变异、系统发育关系和适应性进化提供了见解。这些结果将有助于未来关于该属物种鉴定、种间和种内界定、适应性进化以及系统发育关系的研究。
