Wu Liwei, Fan Panhui, Cai Jiaying, Zang Chenxi, Lin Yulin, Xu Zhichao, Wu Zhengjun, Gao Wei, Song Jingyuan, Yao Hui
State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
College of Life Science, Northeast Forestry University, Harbin, China.
Front Pharmacol. 2024 Mar 7;15:1371390. doi: 10.3389/fphar.2024.1371390. eCollection 2024.
(Fabaceae) species are rich in metabolites and widely used in medicine. Research on the chloroplast genome of is important for understanding its phylogenetics, biogeography, genetic diversity, species identification, and medicinal properties. In this study, comparative genomics and phylogenomics of were analyzed based on the chloroplast genome. The chloroplast genomes of six species were obtained using various assembly and annotation tools. The final assembled chloroplast genome sizes for the six species ranged from 126,380 bp to 129,115 bp, with a total of 109-110 genes annotated. Comparative genomics results showed that the chloroplast genomes of showed typically lacking inverted repeat regions, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. Bioinformatics analysis revealed the presence of 69-96 simple sequence repeats and 61-138 long repeats in the chloroplast genomes. Combining the results of mVISTA and nucleotide diversity, four highly variable regions were screened for species identification and relationship studies. Selection pressure analysis indicated overall purifying selection in the chloroplast genomes of , with a few positively selected genes potentially linked to environmental adaptation. Phylogenetic analyses involving all tribes of Fabaceae with published chloroplast genomes elucidated the evolutionary relationships, and divergence time estimation estimated the chronological order of species differentiations within the Fabaceae family. The results of phylogenetic analysis indicated that species from the six subfamilies formed distinct clusters, consistent with the classification scheme of the six subfamilies. In addition, the inverted repeat-lacking clade in the subfamily Papilionoideae clustered together, and it was the last to differentiate. Co-linear analysis confirmed the conserved nature of chloroplast genomes, and instances of gene rearrangements and inversions were observed in the subfamily Papilionoideae.
豆科植物富含代谢产物，在医学中广泛应用。对其叶绿体基因组的研究对于理解其系统发育、生物地理学、遗传多样性、物种鉴定和药用特性至关重要。在本研究中，基于叶绿体基因组对豆科植物进行了比较基因组学和系统发育基因组学分析。使用各种组装和注释工具获得了六个豆科物种的叶绿体基因组。六个豆科物种最终组装的叶绿体基因组大小在126,380 bp至129,115 bp之间，共注释了109 - 110个基因。比较基因组学结果表明，豆科植物的叶绿体基因组通常缺乏反向重复区域，并且基因组长度、结构、GC含量、密码子使用和基因分布高度相似。生物信息学分析揭示了叶绿体基因组中存在69 - 96个简单序列重复和61 - 138个长重复。结合mVISTA和核苷酸多样性的结果，筛选出四个高变区用于物种鉴定和关系研究。选择压力分析表明豆科植物叶绿体基因组总体上受到纯化选择，少数正选择基因可能与环境适应有关。涉及豆科所有已发表叶绿体基因组的部落的系统发育分析阐明了进化关系，分歧时间估计确定了豆科家族内物种分化的时间顺序。系统发育分析结果表明，六个亚科的物种形成了不同的聚类，与六个亚科的分类方案一致。此外，蝶形花亚科中缺乏反向重复的分支聚集在一起，并且是最后分化的。共线性分析证实了豆科植物叶绿体基因组的保守性质，并且在蝶形花亚科中观察到了基因重排和倒位的实例。
