The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus

Abstract

Background The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants. Results In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum. Conclusion The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.

Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of Kitagawia

“…The complete plastome sequences range in size from 146,718 bp ( K. formosana ) to 148,327 bp ( K. terebinthacea ) for the 14 species of Kitagawia and related taxa ( Table 1 , Figure S1 ). All these plastomes comprised a pair of inverted repeat (IR) regions (17,987–19,043 bp) separated by the large single copy (LSC, 91,829–93,700 bp) and small single copy (SSC) regions (17,377–17,631 bp), exhibiting a typical quadripartite structure [ 43 , 47 ] ( Table 1 , Figure S1 ). The IR regions of three species (17,987 bp for P. morisonii , 18,058 bp for Angelica sylvestris L., and 18,095 bp for C. sinensis ) were the shortest in length ( Table 1 ).…”

“…Plastome sequences can effectively improve the support and resolution of phylogenies at the generic level and beyond [ 41 , 42 , 43 , 44 , 45 , 46 ]. In particular, the plastome-based phylogeny performed by Liu et al [ 47 ] constructed a robust phylogenetic framework for Peucedanum sensu lato and provided a valuable reference to our investigation of Kitagawia . In addition, comparative analyses of plastomes can also provide useful information for eliciting evolutionary and interspecific relationships [ 48 , 49 , 50 ], which should further improve our understanding of the taxonomic classification of Kitagawia .…”

The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

“…Most Seseli species are regional endemics and the composition of the type section of Seseli (i.e., the species closely related to the type species S. tortuosum L.) has not been clearly defined, which leads to imperfect and incomplete classification among Seseli species [ 42 ]. Moreover, given that the genera ( Peucedanum , Ligusticum , and Libanotis ) related to Seseli were also non-monophyly [ 16 , 17 , 28 , 30 ], which made studying the phylogeny and taxonomy of Seseli harder. It is worth noting that many phylogenetic and taxonomic problems of Peucedanum and Ligusticum have been effectively resolved after considering a narrower sense [ 15 , 43 ].…”

“…Plastomes have been widely used in studying the phylogeny of Apiaceae, Ranunculaceae Juss., Saxifragaceae Juss., Allium L., Liliaceae Juss., etc. [27][28][29][30][31][32][33][34][35][36][37]. However, there has been no study on the phylogeny of Seseli based on plastomes and therefore there is ample opportunity to investigate phylogenetic and taxonomic issues of Seseli using plastomes.…”

Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

“…In angiosperm species, chloroplasts are important and common organelles for photosynthesis [ 28 ]. This is due to their unique tetrad structure, high conservation in terms of gene order and gene content [ 29 ], and lower substitution rates than nuclear DNA (especially in regions of inverted repeats) [ 29 , 30 , 31 ], providing a promising solution to phylogenetic uncertainty, especially for taxonomically complex groups [ 32 , 33 ]. Furthermore, the complete chloroplast (cp) genome can be used for screening of DNA barcode sequences [ 34 , 35 , 36 ], species divergence time estimation [ 37 ], evolutionary rate calculation, and environment adaptive analysis [ 38 , 39 ].…”