Phylogeny and Taxonomic Revision of the Genus Melanosciadium (Apiaceae), Based on Plastid Genomes and Morphological Evidence

Melanosciadium is considered a monotypic genus and is also endemic to the southwest of China. No detailed phylogenetic studies or plastid genomes have been identified in Melanosciadium. In this study, the plastid genome sequence and nrDNA sequence were used for the phylogenetic analysis of Melanosciadium and its related groups. Angelica tsinlingensis was previously considered a synonym of Hansenia forbesii. Similarly, Ligusticum angelicifolium was previously thought to be the genus Angelica or Ligusticopsis. Through field observations and morphological evidence, we believe that the two species are more similar to M. pimpinelloideum in leaves, umbel rays, and fruits. Meanwhile, we found a new species from Anhui Province (eastern China) that is similar to M. pimpinelloideum and have named it M. Jinzhaiensis. We sequenced and assembled the complete plastid genomes of these species and another three Angelica species. The genome comparison results show that M. pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis have similarities to each other in the plastid genome size, gene number, and length of the LSC and IR regions; the plastid genomes of these species are distinct from those of the Angelica species. In addition, we reconstruct the phylogenetic relationships using both plastid genome sequences and nrDNA sequences. The phylogenetic analysis revealed that A. tsinlingensis, M. pimpinelloideum, L. angelicifolium, and M. jinzhaiensis are closely related to each other and form a monophyletic group with strong support within the Selineae clade. Consequently, A. tsinlingensis and L. angelicifolium should be classified as members of the genus Melanosciadium, and suitable taxonomical treatments have been proposed. Meanwhile, a comprehensive description of the new species, M. jinzhaiensis, is presented, encompassing its habitat environment and detailed morphological traits.


Introduction
Apioideae, the largest subfamily of Apiaceae, currently consists of approximately 380 genera and 3200 species [1].These species are distributed worldwide, with a concentration in northern temperate regions [2].This subfamily is of great significance as it encompasses a wide range of edible plants containing numerous foods (e.g., Daucus carota and Apium graveolens), herbs (e.g., Levisticum officinale and the species of Angelica L.), and spices (e.g., Coriandrum sativum and Foeniculum vulgare).However, it should be noted that Apioideae also comprises poisonous species (e.g., Conium maculatum and Cicuta viros).Despite the importance and familiarity of many Apioideae members, uncertainties still exist in the classification of this subfamily due to gaps in our understanding of its phylogenetics.
Melanosciadium H. de Boissieu was first published in 1902 and used M. pimpinelloideum as the type of species.Melanosciadium was treated as a monotypic and endemic genus distributed in the southwest of China and, as such, it was in almost all regional Apiaceae treatments [25][26][27].M. pimpinelloideum is also a traditional Chinese medicine that can be used as folk medicine in Hubei Province, China [28].Pimenov's (2006) study of Melanosciadium suggested that the genus should contain three species-M.pimpinelloideum H. de Boissieu (Figure 1A), M. bipinnatum (Shan and F. T. Pu) Pimenov and Kljuykov (Figure 1B), and M. genuflexum Pimenov and Kljukov [29]-and this view persisted in the 2017 publication [30].In addition to Pimenov's research, only Tan et al. (2015) suggested that Pimpinella rhomboidea var.Tenuiloba Shan et Pu has been proposed as a synonym for M. bipinnatum [31].In the previous studies on Angelica and the related species, it can be found that Angelica tsinlingensis K. T. Fu (Figure 1C) is very close to M. pimpinelloideum [32,33].
Angelica tsinlingensis was first described in 1981 and was classified as a species belonging to the genus Angelica L. in both the Flora Reipublicae Popularis Sinicae and the Flora of China [25,26].Liao et al. (2013) conducted phylogenetic studies on Angelica and its Allies based on the nrDNA and cpDNA sequences [32].The results indicated a close relationship between A. tsinlingensis and Melanosciadium pimpinelloideum.However, upon careful examination of the Chinese Apiaceae plant specimens, Pimenov (2017) concluded that A. tsinlingensis should be considered a synonym of Hansenia forbesii (H.Boissieu) Pimenov and Kljuykov [30].This determination was made based on Pimenov's consultation of the aforementioned specimens.After conducting field observations of A. tsinlingensis, M. pimpinelloideum, and H. forbesii, our research prompted us to question the accurate taxonomic classification of A. tsinlingensis.For example, in H. forbesii, the ultimate segments are oblong-ovate, the rays are nearly equal, the petals are pale yellow or yellowish-green, the dorsal and lateral ribs are winged, the wing width is nearly equal, and the endosperm is concave.In contrast, A. Tsinlingensis exhibits distinct characteristics.The median leaflets are rhombic-obovate, and the lateral leaflets are broad-ovate.The rays are extremely unequal, the petals are white, the dorsal ribs are narrow-winged, the lateral ribs are conspicuously wider than the dorsal, and the endosperm plane is slightly concave.Based on these morphological characteristics, we believe that these characteristics are more consistent in the genus Melanosciadium.
Ligusticum angelicifolium Franch.(Figure 1D) was published in 1894 by Franch.Then, according to the fruit morphology study, Leute considered it should be a species in the genus Ligusticopsis Leute, named Ligusticopsis angelicifolia (Franch.)Leute [34].However, Kljuykov argued that it should be the species to which it belongs, and the scientific name of it should be Angelica angelicifolia (Franch.)Kljuykov and Pimenov have identified this species as a member of the Angelica in their respective studies [30,35].In addition, Lavrova has also suggested that Ligusticum angelicifolium may be a synonym of Conioselinum angelicifolium (Franch.)Lavrova [36].Currently, there are two predominant perspectives regarding the nomenclature of this species.One viewpoint advocates for the name Ligusticopsis angelicifolia, while the other argues that it should be referred to as A. angelicifolia.So, after field surveys, consulting specimens, and performing DNA sequencing, we analyzed the location of this species.Ligusticum angelicifolium Franch.(Figure 1D) was published in 1894 by Franch.Then, according to the fruit morphology study, Leute considered it should be a species in the genus Ligusticopsis Leute, named Ligusticopsis angelicifolia (Franch.)Leute [34].However, Kljuykov argued that it should be the species to which it belongs, and the scientific name of it should be Angelica angelicifolia (Franch.)Kljuykov and Pimenov have identified this species as a member of the Angelica in their respective studies [30,35].In addition, Lavrova During our field trips in August 2018, we collected specimens belonging to the Apiaceae family.These specimens were found to be flourishing at elevations ranging from 700 to 1100 m above sea level in Jinzhai County, located in the southwest region of Anhui Province, China.The specimen is similar to Melanosciadium pimpinelloideum.After carefully observing morphological characters and molecular analyses and checking the specimens of Melanosciadium and A. cincta at the online herbariums, we consulted with the relevant floras and literature [25,26].Based on the comprehensive analysis of all available evidence, it is our contention that the observed species can be classified as a novel species belonging to the genus Melanosciadium.Therefore, the present study provides a description and illustration of M. jinzhaiensis (Figure 2). the location of this species.
During our field trips in August 2018, we collected specimens belonging to the Apiaceae family.These specimens were found to be flourishing at elevations ranging from 700 to 1100 m above sea level in Jinzhai County, located in the southwest region of Anhui Province, China.The specimen is similar to Melanosciadium pimpinelloideum.After carefully observing morphological characters and molecular analyses and checking the specimens of Melanosciadium and A. cincta at the online herbariums, we consulted with the relevant floras and literature [25,26].Based on the comprehensive analysis of all available evidence, it is our contention that the observed species can be classified as a novel species belonging to the genus Melanosciadium.Therefore, the present study provides a description and illustration of M. jinzhaiensis (Figure 2).The plastid genome has many features, such as monolepsis, small subfractions, multiple replications, and moderate nucleotide substitution rates [37][38][39][40][41].Despite the highly variable characteristics of the plastid genome, it has the potential to obtain a robust phylogenetic tree [19,21,[42][43][44][45].With the advancement of next-generation sequencing and bioinformatics technologies, obtaining plastid genome data is now more affordable and faster than ever before.As a result, plastid genome sequences have been widely and successfully utilized in plant phylogenetic analyses [46][47][48][49][50].
In this study, we sequenced and assembled the plastid genome sequences of Melanosciadium pimpinelloideum, M. bipinnatum, Angelica tsinlingensis, Ligusticum angelicifolium, the new species M. jinzhaiensis, and another three Angelica species.Then, together with published plastid genome sequences from the family Apiaceae, we reconstructed the phylogenetic position of A. tsinlingensis, L. angelicifolium, and the new species M. jinzhaiensis based on nrDNA sequences and plastid genome sequences.We also performed comparative plastid genome analyses between these species.We provide a taxonomic revision for A. tsinlingensis, L. angelicifolium, and the new species M. jinzhaiensis based on plastid genome comparison and phylogenomic and morphological evidence.

Taxon Sampling
We have collected Melanosciadium pimpinelloideum, M. bipinnatum, Angelica tsinlingensis, Ligusticum angelicifolium, M. jinzhaiensis, and related species.Specimen vouchers are stored in the Herbarium of Sichuan University (SZ; Chengdu, China).The rest of the species sequences for our phylogenetic analysis were obtained from the National Center for Biotechnology Information (NCBI).

Morphological Study
Fruits from the wild specimens of Melanosciadium pimpinelloideum, Angelica tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis were collected for morphological study.Morphological analyses of other characters were based on plants in the wild and herbarium specimens.The anatomical study of the fruit was carried out through a hand section for observation of the details (Figures 3 and 4).No less than 10 seeds were observed for each species.The specimen vouchers are stored in the Herbarium of Sichuan University (SZ), and the corresponding details can be found in Table S1.

nrDNA Sequences and Plastid Genome Sequencing, Assembly, and Annotation
The DNA sequencing was performed using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) at Novogene (Beijing, China) with the Novaseq 150 sequencing strategy.The clean data that remained after processing were assembled using NOVO-Plasty 2.7.1 [51] with the default K-mer value of 39.The rbcL sequence of Melanosciadium

nrDNA Sequences and Plastid Genome Sequencing, Assembly, and Annotation
The DNA sequencing was performed using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) at Novogene (Beijing, China) with the Novaseq 150 sequencing strategy.The clean data that remained after processing were assembled using NOVO-Plasty 2.7.1 [51] with the default K-mer value of 39.The rbcL sequence of Melanosciadium pimpinelloideum (GenBank accession No.: KX527530.1)was used as the initial seed input, and plastid genome sequences of M. pimpinelloideum (GenBank accession No.: MW436383) was used as the reference for these species.Preliminary genome annotation was performed utilizing the PGA program [52].Subsequently, manual adjustments were made to uncertain genes, as well as uncertain start and stop codons, by comparing them with other related plastid genomes using Geneious R11 [53].Protein-coding sequences (CDS) extraction was conducted using the PhyloSuite v1.2.3 software [54].The annotated genome of the species was submitted to the National Center for Biotechnology Information (NCBI), and the accession number was listed in Table S2.Additionally, in order to enhance the reliability of the phylogenetic data, we employed the program GetOrganelle v1.7.5 [55] to extract the nrDNA sequences, which consists of ETS, 18S rRNA, ITS 1, 5.8S rRNA, ITS 2, complete sequence; and 26S rRNA partial sequence.The relevant information and accession number for the National Center for Biotechnology Information (NCBI) of nrDNA sequences are listed in Table S3.

Plastid Genome Comparative Analyses
The sequenced species' annotated genome sequences were submitted to GenBank, and their corresponding accession numbers are listed in Table S2.Circular gene maps of the annotated genomes were performed using the online program Chloroplot (https: //irscope.shinyapps.io/chloroplot/;accessed on 20 December 2023) [56].
The junctions between single-copy regions (LSC region and SSC region) and inverted repeat regions (IRA and IRB regions) among Melanosciadium pimpinelloideum, Angelica tsinlingensis, Ligusticum angelicifolium, M. jinzhaiensis and another three Angelica species (A.dahurica, A. cincta, and A. sylvestris; total 7 species) were compared by using Geneious R11 [53], then visualized it by manually.

Phylogenetic Analysis
In this study, we used nrDNA sequences and cpCDS sequences.Our phylogenetic analyses utilized data from the National Center for Biotechnology Information (NCBI).The data of nrDNA sequences (includes ETS, 18S rRNA, ITS 1, 5.8S rRNA, ITS 2, complete sequence; and 26S rRNA partial sequence) were listed in Table S4, and the data of plastid genome sequences were listed in Table S5.
We used MEGA7 [57] to align DNA sequences with manual adjustment to make sequences more aligned, positioning the gap to minimize nucleotide mismatch.Phylogenetic analyses were carried out employing Maximum Likelihood (ML) and Bayesian Inference (BI) analyses.Before starting, the program MrModeltest version 2.2 [58] was used to select the best model of the ITS sequences and CDS sequences nucleotide substitution.The best model of data I and data II were GTR + G + I for both ML analyses and BI analyses, and the best model of data III was GTR + G for ML analyses and GTR + G + I for BI analyses.Maximum likelihood (ML) analyses were undertaken using RAxML v8.2.4 [59] with 1000 bootstrap replicates.The bootstrap value (BS) is closer to 100%, the more accurate it is.Bayesian Inference (BI) analyses were performed by MrBayes version 3.2 [60].Four simultaneous runs were performed using Markov chain Monte Carlo (MCMC) simulations for 10 million generations.The analysis began with a random tree and sampled one tree every 1000 generations.The first 20% of obtained trees were discarded as "burn-in", and the remaining were used to calculate a majority-rule consensus topology and posterior probability (PP) values.Based on previous analyses, the species Chamaesium H. Wolff and Sanicula L. were chosen as the outgroup [17,61].

Morphological Result
Following a field observation, the fruit morphological characters were investigated and compared to the related species.The results of the morphological study indicate that Melanosciadium jinzhaiensis is similar to M. pimpinelloideum rather than Angelica biserrata, though the new species' specimens were previously identified as A. biserrata (KUN1485850!, NAS00038853!).In our study, we found that the morphological characteristics of M. jinzhaiensis bear a closer resemblance to those of M. pimpinelloideum (Figures 1A and 2; Figures 3A and 4).These similarities encompass leaf forms, leaflets, sheaths, and umbel rays.They share some common characteristics, such as stems purplish, sheaths margin purplish, leaflets rhombic-obovate, bracts often absent, rays very un-equal, etc.
For Angelica tsinlingensis (Figures 1C and 3C), our morphological study reveals that its rays are short and very un-equal, leaflets rhombic-obovate, bracts absent, vittaes abundant, and endosperm concave.We think these characteristics bear a closer resemblance to the attributes exhibited by Melanosciadium.The situation of Ligusticum angelicifolium (Figures 1D and 3D) displayed resemblances to that of A. tsinlingensis and, in fact, was even more pronounced.Pimenov believed that A. Tsinlingensis was the synonym of Hansenia forbesii [30,62].In our field investigation, we found that H. forbesii and A. Tsinlingensis had obvious morphological differences.For example, in H. forbesii, the ultimate segments are oblong-ovate, the rays are nearly equal, the petals are pale yellow or yellowish-green, the dorsal and lateral ribs are winged, the wing width is nearly equal, and the endosperm is concave [25, 26,62].However, A. Tsinlingensis exhibits distinct characteristics.The median leaflets are rhombic-obovate, and the lateral leaflets are broad-ovate.The rays are extremely unequal, the petals are white, the dorsal ribs are narrow-winged, the lateral ribs are conspicuously wider than the dorsal, and the endosperm plane is slightly concave [25,26].These features can be easily distinguished from H. forbesii.According to previous studies and molecular phylogenetic results, we can find that H. forbesii is located in the East Asia Clade, whereas A. Tsinlingensis is located in Selineae [13,14,32,63,64].Consequently, A. Tsinlingensis is a separate species and should belong to the genus Melanosciadium.
The overall morphology of Ligusticum angelicifolium was very similar to that of M. bipinnatum, such as leaf forms, leaflets, umbel rays, and ray number [25, 26,31].And the fruit morphology of L. angelicifolium is more similar to that of A. tsinlingensis and M. jinzhaiensis (Figures 3 and 4).These species can be easily distinguished by mericarps characters, and the main morphological differences of these species are summarized in Table 1.

Plastid Genome Comparation Results
These total seven species' plastid genomes presented a single and typical quadripartite circular structure (Figure 5) that was divided into four regions: two inverted repeat regions (IRs), a large single-copy region (LSC), and a small single-copy region (SSC).The size of the plastid genomes of three Angelica species (A.dahurica, A. cincta, and A. sylvestris) ranged from 146,138 bp (A.sylvestris) to 146,847 bp (A.dahurica).And according to a previous study [49,65], the size of the plastid genomes of Angelica is around 147,000 bp.However, the size of the plastid genomes in Melanosciadium pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis are as follows: A. Tsinlingensis is 163,608 bp, L. angelicifolium is 163,798 bp, M. pimpinelloideum is 164,329 bp, and M. jinzhaiensis is 164,544 bp, respectively.These four species are very similar in size.Large differences in genome size led to differences in the number of genes.In three Angelica species (A.dahurica, A. cincta, and A. sylvestris), including a total of one hundred and twenty-nine genes (eightyfour protein-coding genes, thirty-six transfer RNA genes, eight ribosomal RNA genes, and one pseudogene), while the remaining four species (M.pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis) including a total of one hundred and forty-four genes (ninety-eight protein-coding genes, thirty-seven transfer RNA genes, eight ribosomal RNA genes, and one pseudogene).They shared one hundred and fourteen unique genes, including eighty protein-coding genes, thirty transfer RNA genes, four ribosomal RNA genes, and one pseudogene (Table 2).The length of small single-copy regions (SSC) of all these seven species is consistent; this result is similar to previous plastid genome research on Apioideae (Apiacea) [18][19][20][21]49,66,67]. In contrast to the SSC regions, the large single-copy regions (LSC) showed significant variation.In three Angelica species (A.dahurica, A. cincta, and A. sylvestris), the LSC regions ranged from 93,297 bp (A.cincta) to 93,539 bp (A.dahurica).The length of the LSC regions for the other four species is 76,649 bp (A.tsinlingensis), 76,900 bp (Ligus- The species name and specific information regarding the genome (length, GC content, and the number of genes) are depicted in the center of the plot.The length of the corresponding single short copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions is also given.Genes are color-coded by their functional classification.Represented with arrows, the transcription directions for the inner and outer genes are listed clockwise and anticlockwise, respectively.The optional shaded area stretching from the inner sphere toward the outer circle marks the IR regions.The length of small single-copy regions (SSC) of all these seven species is consistent; this result is similar to previous plastid genome research on Apioideae (Apiacea) [18][19][20][21]49,66,67]. In contrast to the SSC regions, the large single-copy regions (LSC) showed significant variation.In three Angelica species (A.dahurica, A. cincta, and A. sylvestris), the LSC regions ranged from 93,297 bp (A.cincta) to 93,539 bp (A.dahurica).The length of the LSC regions for the other four species is 76,649 bp (A.tsinlingensis), 76,900 bp (Ligusticum angelicifolium), 76,578 bp (Melanosciadium jinzhaiensis), and 76,450 bp (M.pimpinelloideum).This is caused by the expansion of the IR regions.The expansion and contraction of IR regions are important for variations in genome size and play a crucial role in plant evolution [18,61,[68][69][70].
In our study, the IR regions ranged from 17,817-18,058 bp in the three Angelica species (A.dahurica, A. cincta, and A. sylvestris), while the length of IR regions in these four species is 34,705 bp (A.tsinlingensis), 34,717 bp (Ligusticum angelicifolium), 35,212 and 35,215 bp (Melanosciadium jinzhaiensis), and 34,717 bp (M.pimpinelloideum), respectively.Meanwhile, the junctions of the IR/LSC have changed, and the junctions of the IR/SSC are consistent.We illustrated the junctions of IR/LSC and IR/SSC and designated J LA (LSC/IRA), J LB (LSC/IRB), J SA (SSC/IRA), and J SB (SSC/IRB) (Figure 6).Junctions J SB and J SA are consistently positioned across all species: J SB is in between the pseudogene ψycf1 and the ndhF gene, and J SA occurs in the ycf1 gene.In three Angelica species (A.dahurica, A. cincta, and A. sylvestris), junction J LB occurs in the ycf2 gene, and junction J LA between the trnL-CAA gene and trnH-GUG gene.But in the other four species (M.pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis), junction J LB occurs in the petB gene and junction J LA between the petD gene and trnH-GUG gene.
In our study, the IR regions ranged from 17,817-18,058 bp in the three Angelica species (A.dahurica, A. cincta, and A. sylvestris), while the length of IR regions in these four  In conclusion, we observed similarities in the plastid genome size, gene number, and length of the LSC and IR regions among the four species: M. pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis.The plastid genomes of these species are distinct from those of the three Angelica species (A.dahurica, A. cincta, and A. sylvestris).

Phylogenetic Result
For nrDNA sequences, the phylogenetic results are presented in Figure 7.The topological consistency of the phylogenetic tree is derived from Bayesian Inference (BI) and Maximum Likelihood (ML) analyses.Only the BI tree is depicted in Figure 7, accompanied In conclusion, we observed similarities in the plastid genome size, gene number, and length of the LSC and IR regions among the four species: M. pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis.The plastid genomes of these species are distinct from those of the three Angelica species (A.dahurica, A. cincta, and A. sylvestris).

Phylogenetic Result
For nrDNA sequences, the phylogenetic results are presented in Figure 7.The topological consistency of the phylogenetic tree is derived from Bayesian Inference (BI) and Maximum Likelihood (ML) analyses.Only the BI tree is depicted in Figure 7, accompanied by bootstrap support values derived from ML analyses.The phylogenetic exhibited that Melanosciadium jinzhaiensis, M. pimpinelloideum, M. bipinnatum, Angelica tsinlingensis, and Ligusticum angelicifolium formed a monophyletic group with robust support (Bayesian inference posterior probability, BI = 0.99; maximum parsimony bootstrap, ML = 67%).This monophyletic group is sister to Angelica and is located in the Selineae [13,14,32,71].
by bootstrap support values derived from ML analyses.The phylogenetic exhibited that Melanosciadium jinzhaiensis, M. pimpinelloideum, M. bipinnatum, Angelica tsinlingensis, and Ligusticum angelicifolium formed a monophyletic group with robust support (Bayesian inference posterior probability, BI = 0.99; maximum parsimony bootstrap, ML = 67%).This monophyletic group is sister to Angelica and is located in the Selineae [13,14,32,71].Our cpCDS sequences of plastid genome phylogenetic analyses used the NCBI data.The data are listed in Table S5.The phylogenetic trees derived from BI and ML analyses were topologically consistent.Thus, only the BI tree is shown in Figure 8, with bootstrap support values obtained from ML analyses.The phylogenetic tree of plastid genomes also showed these five species (Melanosciadium jinzhaiensis, M. bipinnatum, M. pimpinelloideum, Angelica tsinlingensis, and Ligusticum angelicifolium) formed a monophyletic group with the best support (Bayesian inference posterior probability, BI = 1.00; maximum parsimony bootstrap, ML = 100%).The monophyletic group is also a sister to Angelica within the Selineae clade [13,14,32,71].

Etymology
The specific epithet refers to the type locality, Jinzhai County of Anhui Province in China.Phenology Flowering from July to September and fruiting from August to October.Distribution, habitat, and ecology This species is currently known little from the Herbariums, only located in the type locality, Jinzhai County of Anhui Province in China.According to its natural environment, we speculate that it may grow in the forests of eastern Anhui, western Hubei, and northern Jiangxi at an altitude of 700-1500 m.This species grows in the humid environment under the forests.Endemic to China.
Phenology Flowering occurs from August to September, and fruiting occurs from September to October.

Figure 5 .
Figure 5. Chloroplast genome map of Angelica sylvestris (the left) and Melanosciadium pimpinelloideum (the right).The species name and specific information regarding the genome (length, GC content, and the number of genes) are depicted in the center of the plot.The length of the corresponding single short copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions is also given.Genes are color-coded by their functional classification.Represented with arrows, the transcription directions for the inner and outer genes are listed clockwise and anticlockwise, respectively.The optional shaded area stretching from the inner sphere toward the outer circle marks the IR regions.

Figure 5 .
Figure 5. Chloroplast genome map of Angelica sylvestris (the left) and Melanosciadium pimpinelloideum (the right).The species name and specific information regarding the genome (length, GC content, and the number of genes) are depicted in the center of the plot.The length of the corresponding single short copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions is also given.Genes are color-coded by their functional classification.Represented with arrows, the transcription directions for the inner and outer genes are listed clockwise and anticlockwise, respectively.The optional shaded area stretching from the inner sphere toward the outer circle marks the IR regions.

species is 34 ,
705 bp (A.tsinlingensis), 34,717 bp (Ligusticum angelicifolium), 35,212 and 35,215 bp (Melanosciadium jinzhaiensis), and 34,717 bp (M.pimpinelloideum), respectively.Meanwhile, the junctions of the IR/LSC have changed, and the junctions of the IR/SSC are consistent.We illustrated the junctions of IR/LSC and IR/SSC and designated JLA (LSC/IRA), JLB (LSC/IRB), JSA (SSC/IRA), and JSB (SSC/IRB) (Figure6).Junctions JSB and JSA are consistently positioned across all species: JSB is in between the pseudogene ψycf1 and the ndhF gene, and JSA occurs in the ycf1 gene.In three Angelica species (A.dahurica, A. cincta, and A. sylvestris), junction JLB occurs in the ycf2 gene, and junction JLA between the trnL-CAA gene and trnH-GUG gene.But in the other four species (M.pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis), junction JLB occurs in the petB gene and junction JLA between the petD gene and trnH-GUG gene.