背景:飞燕草属是一种分类学上复杂的属,具有重要的系统发育和经济重要性。尽管叶绿体基因组数据集很少,对该属基因组结构和选择压力的全面了解仍然未知。此外,该属中的几个类群仅在新疆发现,中国,以中国和中亚飞燕草物种的分布和多样性而闻名的地区。因此,研究该地区叶绿体基因组的特征将为该属的进化过程和系统发育关系提供有价值的见解。
结果:在这项研究中,检查了八个新完成的叶绿体基因组,长度从153,979bp到154,284bp不等。除了这些,分析了在Delphinium中重新注释的六个先前报告的分类单元,在所有样品中鉴定了111个独特的基因。基因组结构,简单序列重复和短分散重复的分布,这些飞燕草类群的基因含量相似。九个高变基因间间隔区和蛋白质编码区,包括ndhF-trnL(TAG),rpl16-内含子,rpl33,rps15,rps18,trnK(TTT)-trnQ(TTG),trnP(TGG)-psaJ,trnT(GGT)-psbD和ycf1在13个多年生飞燕草中鉴定。所有质体基因的选择压力和密码子使用偏好在14个Delphinium类群中进行。基于14个飞燕草质体的系统发育分析,与两个乌头(毛茸茸科)物种一起作为外群类群,揭示了飞燕草的单系性质。我们的发现进一步将飞燕分为两个不同的进化枝:多年生物种(进化枝I)和一年生物种(进化枝II)。此外,与nrDNAITS拓扑相比,细胞学数据和形态特征,D.mollifolium和D.maackianum显示出可能参与杂交或多倍体化过程。除了这两个物种,多年生飞燕草(进化枝I)与利用种子形态的基于形态的系统具有更强的一致性。
结论:这项研究首次全面分析了飞燕草类群的体体变异,根据对14个完整的石膏体的检查。飞燕草的叶绿体基因组结构与其他被子植物相似,具有典型的四体结构,具有保守的基因组排列和基因特征。此外,非编码区的变异大于叶绿体基因组的编码区。通过飞燕草质体之间的DNA序列差异以及随后的系统基因组分析,ndhF-trnL(TAG)和ycf1被鉴定为有前途的分子标记。这些高度可变的基因座对飞燕草的未来系统发育和系统地理学研究具有重要的潜力。我们基于整个质体的系统发育分析,132个独特的基因间间隔区的串联,77个独特的蛋白质编码基因和nrDNAITS的串联,所有这些都支持飞燕草的单系和多年生类群群在该属中的一个进化枝。这些发现为系统的,属的系统发育和进化研究,以备将来研究。
BACKGROUND: Delphinium L. represents a taxonomically intricate genus of significant phylogenetic and economic importance in Ranunculaceae. Despite the existence of few chloroplast genome datasets, a comprehensive understanding of genome structures and selective pressures within the genus remains unknown. Furthermore, several taxa in this genus are exclusively found in Xinjiang, China, a region renowned for its distribution and diversity of Chinese and Central Asian Delphinium species. Therefore, investigating the features of chloroplast genomes in this area will provide valuable insights into the evolutionary processes and phylogenetic relationships of the genus.
RESULTS: In this study, the eight newly completed chloroplast genomes are examined, ranging in length from 153,979 bp to 154,284 bp. Alongside these, analysing six previously reported taxa re-annotated in Delphinium, 111 unique genes are identified across all samples. Genome structure, distributions of simple sequence repeats and short dispersed repeats, as well as gene content are similar among these Delphinium taxa. Nine hypervariable intergenic spacers and protein coding regions, including ndhF-trnL(TAG), rpl16-intron, rpl33, rps15, rps18, trnK(TTT)-trnQ(TTG), trnP(TGG)-psaJ, trnT(GGT)-psbD and ycf1, are identified among 13 perennial Delphinium. Selective pressure and codon usage bias of all the plastid genes are performed within 14 Delphinium taxa. Phylogenetic analysis based on 14 Delphinium plastomes, alongside two Aconitum (Ranunculaceae) species serving as outgroup taxa, reveals the monophyletic nature of Delphinium. Our findings further discern Delphinium into two distinct clades: perennial species (clade I) and annual species (clade II). In addition, compared with the nrDNA ITS topology, cytological data and morphological characters, D. mollifolium and D. maackianum showed potential involvement in hybridization or polyploidization processes. Excluding these two species, the perennial Delphinium (clade I) exhibits a stronger consistency with the morphology-based system that utilized seed morphology.
CONCLUSIONS: This study represents the first comprehensive analysis of plastomic variations among Delphinium taxa, based on the examination of 14 complete plastomes. The chloroplast genome structure of Delphinium is similar to other angiosperms and possesses the typical quadripartite structure with the conserved genome arrangement and gene features. In addition, the variation of non-coding regions is larger than coding regions of the chloroplast genome. Through DNA sequence divergence across Delphinium plastomes and subsequent phylogenomic analyses ndhF-trnL(TAG) and ycf1 are identified as promising molecular markers. These highly variable loci held significant potential for future phylogenetic and phylogeographic studies on Delphinium. Our phylogenomic analyses based on the whole plastomes, concatenation of 132 unique intergenic spacer regions, concatenation of 77 unique protein-coding genes and nrDNA ITS, all support the monophyly of Delphinium and perennial taxa clusters together into one clade within this genus. These findings provide crucial data for systematic, phylogenomic and evolutionary research in the genus for future studies.