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

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. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-022-03488-x.

genus is extremely heterogenous and exhibits great diversity in life-forms, leaf and fruit structures, and chemical constituents [9]. Hence, several researchers are prone to divide this genus into smaller and presumably more natural units. For example, Pimenov and Leonov [5] suggested that all members of Peucedanum except 8-10 species included in sect. Peucedanum should be transferred to other genera. Based on morphological and phytochemical evidences, Reduron et al. [10] separated the genera Cervaria Wolf, Imperatoria L., Oreoselinum Mill., Pteroselinum Rchb., Thysselinum Adans., Xanthoselinum Schur and Holandrea Reduron from Peucedanum. Winter et al. [11] established three new genera (Afrosciadium P.J.D. Winter, Nanobubon Magee and Notobubon B.-E. van Wyk) to accommodate the African peucedanoid species and transferred 24 Peucedanum species into Afroligusticum C. Norman, Cynorhiza Eckl. & Zeyh., and Lefebvrea A. Rich. However, due to the varied morphological features of leaf division, bracteoles, and mericarps, distinguishing separate genera from Peucedanum is extremely difficult [2,3]. Therefore, the generic limits of Peucedanum based on morphological characters faces challenges.
A robust phylogenetic framework could provide a valuable information to aid the generic delimitation of Peucedanum. Previously, a few molecular phylogenies of Peucedanum based on single or multiple-locus DNA sequence data, such as nuclear ribosomal DNA internal transcribed spacer (ITS), plastid DNA rpl16 and rps16 intron, have been performed, yet these analyses failed to recognize Peucedanum as a monophyletic group [2,[12][13][14][15][16]. This phenomenon infers that re-evaluating the generic limits of Peucedanum may be essential. Nevertheless, weak supports and low resolutions of these phylogenetic trees could not provide sufficient information to support the improvement of taxonomy for Peucedanum. Therefore, additional molecular data are urgent to reconstruct a strong phylogeny.
In addition, several species of Peucedanum are highly appreciated as traditional medicinal herbs due to their versatile therapeutic properties [17]. Among them, Peucedanum praeruptorum Dunn, known as "Baihu Qianhu", is an excellent representation. The dried root of P. praeruptorum has been utilized as traditional Chinese medicine for more than 1500 years, which is generally used to treat respiratory diseases, pulmonary hypertension, chest pain, as well as symptomatic coughs and dyspnea [18]. However, most Peucedanum species exhibit abundant intraspecific variations in morphology that make it difficult to accurately identify species. In order to assure medicinal quality, it is, therefore, necessary to develop specific DNA marker for Peucedanum species authentication.
The plastid genome (plastome) is one of the three DNA genomes (with nuclear and mitochondrial genomes) in plants. The genome is uniparentally inherited, lacks recombination, and possesses highly variable characters in flowering plants; hence, it has the potential to significantly improve the supports and resolutions of the phylogeny [19][20][21][22]. Furthermore, a typical plastome comprises two inverted repeats regions (IRs) of 22-25 kb separated by the large single copy region (LSC) of 82-90 kb and small single copy region (SSC) of 15-20 kb and generally encodes 110-130 unique genes [23,24]. Comparative analysis of plastome could reveal the diversity of plastome in structural organization, gene arrangement and content that deepens our understanding of adaptive evolution for plant lineages and identify suitable mutation hotspots for species authentication [21,25,26]. Hence, with the development of next-generation sequencing and bioinformatics technologies, plastomes have been extensively and successfully used for plant phylogenetic analyses and development of specific DNA barcodes in recent years [25][26][27][28][29][30][31][32].
Currently, although six plastomes of Peucedanum species were submitted in GenBank [33][34][35][36], the plastid phylogenomic analysis of the genus has not been conducted. In this study, we newly sequenced the plastomes of seven Peucedanum taxa. In conjunction with the previously reported five plastomes of Peucedanum, we carried out a comprehensive analysis of plastomes for this taxonomically difficult plant group. Our aims were to: (1) investigate the plastome features of Peucedanum plants; (2) screen out suitable mutation hotspot regions from plastome as candidate DNA barcodes for species identification of Peucedanum; (3) test the power of plastome for improving the supports and resolutions of phylogeny in the complex Peucedanum genus. Overall, our results will well lay the foundation for the phylogenetic and taxonomic studies of Peucedanum.

Plastome features of Peucedanum
Illumina sequencing generated 36,875,778-44,140,972 paired-end clean reads for the seven Peucedanum samples. Among them, 712,889 to 6,125,929 reads were mapped to the final assembly. Based on these data, we obtained seven high-quality Peucedanum plastomes, with coverage ranging from 730.073× to 6,266.178× (Table S1).
In order to analyze the codon usage of Peucedanum plastomes, 79 protein-coding genes were extracted and connected for each plastome. These sequences were 66,552-68,130 bp in length and encoded 22,184-22,710 codons. The Leu was encoded by the highest number of codons (2,347-2,404), while the Cys was the least (234-243) in all plastomes (Table S3). In addition, relative synonymous codon usage (RSCU) values of all codons ranged from 0.32 to 2.01 in the twelve plastomes (Table S3). Specifically, RSCU values of 30 codons were greater than 1.00 in all plastomes, whereas the codon AUA with RSCU > 1.00 was only detected in P. insolens plastomes (Fig. 2). All codons with RSCU > 1.00 were ended with A/U, except UUG (Fig. 2).
The potential RNA editing sites for 35 protein-coding genes of the twelve plastomes were detected. A total of 56-60 potential RNA editing sites were identified (Table S4, Fig. S1). All detected RNA editing sites were Cytosine to Uracil (C-U) conversion and most of them occurred in the second codon position (42)(43)(44)(45), followed by the first codon position (12)(13)(14)(15)(16), but no sites situated in the third codon position (Fig. S1A). Moreover, the ndhB gene contained the highest number of RNA editing sites ranging from 10 to 11 (Fig. S1B).
The total number of SSRs ranged from 58 to 89 among the twelve Peucedanum plastomes (Fig. 3, Table S5). Most of the SSRs distributed in the LSC region for all plastomes (Fig. 3A). Among these SSRs, the mononucleotide repeats were the most abundant , followed by the dinucleotides (14-21) (Fig. 3B). In addition, bases A and T were the dominant elements for all identified SSRs in the twelve plastomes.

Plastome comparison and hotspots identification
The borders of IRa/SSC, IRb/SSC, and IRb/LSC among the twelve Peucedanum plastomes were slightly conserved: the IRa/SSC junctions of most samples were located between ycf1 gene and ndhF gene, but expanded into ndhF gene in P. delavayi and P. angelicoides; the boundaries of IRb/SSC fell into ycf1 gene; the IRb/LSC borders of most samples were located between genes of trnL and trnH, but extremely expanded into psbA gene in P. angelicoides (Fig. 4). However, the junctions of IRa/LSC of plastomes within Peucedanum genus were divergent and could be classified into four different types. The junctions of IRa/LSC fell into the rps19 gene in P. delavayi and P. insolens, belonging to the type I; the IRa/LSC borders contracted to the intergenic region of trnL-trnH in P. angelicoides (type II) while moved to the intergenic regions of rpl2-trnI in P. mashanense Shan et Sheh and P. medicum Dunn (type III); the IRa/LSC borders of most remainder Peucedanum plants fell into the ycf2 gene, but contracted to the intergenic regions of ycf2-trnL in P. chujaense K. Kim (Fig. 4).

Phylogenetic analyses
The analyses of ML and BI generated the identical tree topology. The Fig. 8

Comparison of the plastomes in Peucedanum
In this study, we sequenced and assembled seven plastomes of Peucedanum and performed a comprehensive comparative analyses of these plastomes with five other published plastomes of this genus obtained from GenBank. All Peucedanum plastomes showed a typically quadripartite structure, including a pair of inverted repeats regions separated by the large single copy region and small single copy region [33][34][35][36]. In addition, codon bias, RNA editing sites, and the distribution and constituent of SSRs were quite similar among twelve Peucedanum plastomes. These results suggested that Peucedanum plastome is conserved in terms of genome structure, codon bias, RNA editing sites, and SSRs. It is worth noting that this phenomenon is commonly found in other genera of flowering plants [38][39][40], which may be related to maintaining the stability of plastome function. However, we also detected obvious diversity among the twelve Peucedanum plastomes. First, the overall sizes of plastomes varied from 142,494 bp (P. angelicoides) to 156,899 bp (P. insolens) among Peucedanum plants. Second, the ycf15 gene was lost in P. delavayi and P. insolens, whereas the trnT-GGU gene was absent in P. praeruptorum and P. harry-smithii var. grande. The loss of the ycf15 gene has been detected in a wide diversity of lineages in the angiosperms [41][42][43][44], which may occur independently during the evolution of these lineages, hence, it may not provide relevant phylogenetic information. However, the loss of trnT-GGU gene was only observed in P. praeruptorum and P. harry-smithii var. grande and not identified in other members of Apiaceae [26,37,39], and thus it can be used as specific molecular marker to recognize this group. Third, the inversion of the trnY-trnD-trnE gene was detected in P. japonicum and P. medicum, which has been observed in Angelica L. species [26]. Finally, we observed extensive expansion and contraction of the IR regions among Peucedanum samples, recognizing four types of SC/IR border. All patterns have been observed in other genera of Apiaceae [26,37,39]. Overall, these plastome divergences detected among Peucedanum members further implied the non-monophyly of the Peucedanum genus.

Phylogeny inference
The utilization of a small number of DNA fragments for phylogenetic analysis may cause phylogenetic errors and thus result in the incongruent topology among different DNA sequences [45][46][47]. Hence, using few DNA sequences to infer the phylogeny of plant species might be frequently insufficient and inappropriate, especially at low taxonomic levels [26,47]. The plastome sequence possesses highly variable characters and thus has the tremendous potential power to reconstruct the robust phylogeny at low taxonomic levels [19][20][21][22]31]. Therefore, we performed plastid phylogenomic analyses for Peucedanum genus in this study. As expected, compared to previous phylogenetic studies by using single or multiple locus DNA sequences [2,[12][13][14][15][16], our phylogenetic analyses based on whole plastome sequences generated a robust phylogenetic framework for Peucedanum members, all nodes showing PP = 1.00 and BS ≥ 96. This result justifies that the plastome sequence is powerful and effective to improve the supports and resolutions of phylogeny for Peucedanum genus. The Peucedanum genus was not recovered as monophyletic in our phylogenomic analyses, which was congruent with the previous studies that used ITS data and two plastid DNA regions (rpl16 and rps16 intron) [2,[12][13][14][15][16]. It is further supported by the great divergence of leaf epidermal morphologies [48], and fruit structures [49,50] among Peucedanum members. These results justified that the Peucedanum genus is not a natural taxonomy unit. Therefore, the current taxonomy system of Peucedanum urgently needs to be improved and revised. Although the taxonomic treatment for Peucedanum members has not been performed in the current study due to the absence of the type species of Peucedanum (P. officinale L.), our results lay the foundations for the future taxonomic studies of Peucedanum.
The phylogenetic relationships among P. japonicum, P. praeruptorum, and P. terebinthaceum have long been controversial [14,51,52]. The phylogenetic analyses of Feng et al. [14] based on ITS sequences showed that P. praeruptorum was sister to P. japonicum that was relatively distant from P. terebinthaceum. However, the results of Ostroumova et al. [51] and Pimenov et al. [52] indicated that P. praeruptorum made a cluster with P.
terebinthaceum being sister to P. japonicum. Our plastid phylogenomic analyses robustly supported that P. japonicum was sister to the clade consisting of P. ampliatum, P. praeruptorum and P. harry-smithii var. grande, in which the subclade of P. praeruptorum + P. harry-smithii var. grande diverged from P. ampliatum; P. terebinthaceum and P. chujaense clustered into a clade that was distant from all other Peucedanum members. The relationships recovered in the current study are different from those of previous studies [14,51,52]. With high supports and resolutions, our plastid-based phylogenetic analyses provide new sights into the inter-species relationship within Peucedanum.

Potential DNA barcodes
The accurate species identification has always been a serious challenge faced by taxonomists. The advent of DNA barcoding technology, which uses the short DNA sequences with sufficient variations to discriminate species [53], promises to resolve this difficulty. The mitochondrial gene cytochrome oxidase 1 has been proven to be effective and reliable as a standard DNA barcode for animal species identification [54][55][56][57]. However, in plants, Fig. 6 Sequence identity plots for the twelve Peucedanum plastomes reliable species identification based on universal DNA barcodes, i.e., rbcL, matK, trnH-psbA, is frequently problematic [58][59][60][61][62]. As expected, we found that the variation in rbcL gene was relatively low (Pi = 0.00925) among Peucedanum plants. Hence, this region may have limited power to discriminate Peucedanum species.

Conclusion
This study is the first attempt to comprehensively investigate the plastome features and infer phylogeny by using plastome data for Peucedanum genus. Comparative analyses found that plastomes of Peucedanum are conserved 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. The plastid phylogenomic analyses prove that plastome data are efficient and powerful for improving the supports and resolutions of Peucedanum phylogeny and robustly support that Peucedanum is not a monophyletic group. In addition, fifteen mutation hotspot regions are identified across the plastomes that can serve as potential DNA barcodes for species identification in Peucedanum. Overall, our study lays the foundations for the future phylogeny and taxonomy of Peucedanum.

Plant material, DNA extraction, plastome sequencing and assembly
The fresh young leaves of seven Peucedanum taxa were collected from the wild and the greenhouse in College of Life Sciences, Sichuan University, and then dried with silica gel. The formal identifications of all samples were undertaken by Professor Xingjin He (Sichuan University). The voucher specimens were deposited at the herbarium of Sichuan University (Chengdu, China) under deposition numbers of LCK2020001-LCK2020004, LZL2020085, JQP19082303, and JQP19082505 (Table S6). Total DNA was extracted from ~20 mg silicagel-dried leaves with the CTAB method [71]. Genomic DNA then was fragmented into 400 bp to construct the pair-end library, following the manufacturer's protocol (Illumina, San Diego, CA, USA). The libraries were sequenced on the Illumina NovaSeq platform at Personalbio (Shanghai, China). Raw data were filtered using fastP v0.15.0 (-n 10 and -q 15) to obtain high quality reads [72]. Then high-quality reads were used to assemble the whole plastome with NOVOPlasty v2.6.2 [73], with the default parameters and rbcL sequence from P. japonicum (JF943288) as seed.

Identification of divergence hotspots
In order to identify mutation hotspot regions, the protein coding genes, non-coding regions and intron regions of the twelve Peucedanum plastomes were extracted in Geneious v9.0.2 [75] and aligned with MAFFT v7.221 [81]. Then, alignments with more than 200 bp in length were used to evaluate nucleotide diversity (Pi) using DnaSP v5.0 [82]. The thresholds of Pi for protein coding gene and non-coding region were set as 0.01200 and 0.03100, respectively.

Phylogenetic analyses
To infer the phylogenetic relationships among Peucedanum species, we reconstructed phylogenetic trees using 39 plastomes (Table S6, Table S7). Cicuta virosa L. and Cryptotaenia japonica Hassk. were chosen as outgroup to root the phylogenetic tree, according to the results of Wen et al. [37]. Sequence alignment was performed with the software MAFFT v7.221 [81], and adjusted and corrected manually when necessary. The unambiguous matrix was subjected to Maximum-Likelihood analyses (ML) and Bayesian Inference (BI). The ML phylogenetic tree was reconstructed in the program RAxML v8.2.8 [83] with 1000 replicates and GTRGAMMA model as the RAxML manual suggested. The BI analysis was performed by using MrBayes v3.2.7 [84] with the best-fit substitution model (TVM+I+G) determined by Modeltest v3.7 [85]. Two independent Markov chains were run for 1,000,000 generations, sampling every 100 generations. The first 25% of trees were discarded as burn-in and the remainder were used to generate the consensus tree. Results of phylogenetic analyses were visualized and edited in FigTree v1.4.2 [86].

Funding
This work was supported by the National Natural Science Foundation of China (Grant No. 32170209, 32070221, 31872647), National Herbarium of China, National Herbarium resources teaching specimen database (Grant No. 2020BBFK01). The funders were not involved in the design of the research, collection, analysis and interpretation of data, and manuscript preparation.

Availability of data and materials
The seven newly sequenced plastomes have been submitted into NCBI with accession numbers: OK336473-OK336479.

Declarations
Ethics approval and consent to participate Collection of all samples completely complies with national and local legislation permission. Plant samples used in the study were not included in the list of national key protected plants and not collected from national park or natural reserve. According to national and local legislation, no specific permission was required for collecting these plants.

Consent for publication
Not applicable.