Qin Qian, Dong Yanjing, Chen Jialong, Wang Bo, Peng Yuxin, Zhang XinPeng, Wang Xiaoyun, Zeng Jinxiang, Zhong Guoyue, Zhang Shouwen, Du Xiaolang
Chinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese Medicine, Nanchang, 330004, China.
BMC Plant Biol. 2025 Feb 6;25(1):157. doi: 10.1186/s12870-025-06138-0.
The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), the emergence of the Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, the molecular evolution and phylogenetic relationships within Pap. remain poorly resolved due to limited molecular data and incomplete research, highlighting the need for systematic investigation.
This study presents an in-depth analysis of the cpDNAs within the Pap., with the aim of unraveling the molecular evolution and phylogenetic interconnections among its species.
Complete cpDNAs of 18 Pap. species were sequenced using the Illumina Novaseq 6000 platform, followed by assembly and annotation. Comparative genomic analyses were conducted to elucidate structural variations and phylogenetic relationships.
The research has uncovered significant differences in the structure and characteristics of the cpDNAs within the Pap.. The lengths of the cpDNAs of 18 species range from 121,190 bp to 158,539 bp, and they contain between 107 and 112 unique genes. Five species, namely Desmodium elegans and Indigofera bracteata, exhibit a typical quadripartite structure, while thirteen species from genera such as Astragalus (Ast.), Hedysarum (Hed.), and Caragana (Car.) are grouped within the Inverted Repeat-Lacking Clade (IRLC). Genetic characteristic analysis revealed a plentiful presence of SSR loci, with single-nucleotide repeats and dinucleotide (A/T) repeats being the most predominant. Notably, the cpDNAs of five species including D. elegans have experienced significant rearrangements. For example, an inversion of approximately 23 kilobase (kb) pairs was observed in Pueraria peduncularis and Sophora moorcroftiana. These species exhibit pronounced differences in their non-coding regions. Comparative genomic variations at cpDNA sites were identified. Moreover, by using D. elegans as a reference, six genes (ycf4, clpP, ycf1, trnI-GAU, accD, rpl32) displayed high nucleotide polymorphism (Pi > 0.1), and the Ka/Ks ratio for all protein-coding genes was determined to be less than 1. The topological structure of the constructed phylogenetic tree of 85 species was basically consistent with that of Pap.. Seven main clades were formed and relatively high bootstrap values were exhibited, further clarifying the evolutionary relationships among them.
This study provides novel insights into the molecular evolution and phylogeny of Pap., offering a foundational resource for future taxonomic and evolutionary research.
豆科(Fab.)叶绿体基因组(cpDNA)的结构经历了重大的进化修饰。在蝶形花亚科(Pap.)中,缺乏反向重复序列分支(IRLC)的出现代表了一种主要的基因组改变。然而,由于分子数据有限和研究不完整,蝶形花亚科内的分子进化和系统发育关系仍未得到很好的解决,这突出了进行系统研究的必要性。
本研究对蝶形花亚科内的cpDNA进行了深入分析,旨在揭示其物种间的分子进化和系统发育联系。
使用Illumina Novaseq 6000平台对18种蝶形花亚科植物的完整cpDNA进行测序,随后进行组装和注释。进行比较基因组分析以阐明结构变异和系统发育关系。
该研究发现了蝶形花亚科内cpDNA在结构和特征上的显著差异。18个物种的cpDNA长度从121,190 bp到158,539 bp不等,包含107至112个独特基因。五个物种,即雅致山蚂蝗和苞叶木蓝,呈现出典型的四分体结构,而黄芪属(Ast.)、岩黄耆属(Hed.)和锦鸡儿属(Car.)等属的13个物种则归类于缺乏反向重复序列分支(IRLC)。遗传特征分析显示SSR位点丰富,单核苷酸重复和二核苷酸(A/T)重复最为常见。值得注意的是,包括雅致山蚂蝗在内的五个物种的cpDNA经历了重大重排。例如,在短梗葛和川西槐中观察到约23千碱基(kb)对的倒位。这些物种在非编码区表现出明显差异。鉴定了cpDNA位点的比较基因组变异。此外,以雅致山蚂蝗为参考,六个基因(ycf4、clpP、ycf1、trnI-GAU、accD、rpl32)显示出高核苷酸多态性(Pi>0.1),并且所有蛋白质编码基因的Ka/Ks比值均小于1。构建的85个物种的系统发育树的拓扑结构与蝶形花亚科的基本一致。形成了七个主要分支,并显示出相对较高的自展值,进一步阐明了它们之间的进化关系。
本研究为蝶形花亚科的分子进化和系统发育提供了新的见解,为未来的分类学和进化研究提供了基础资源。