https://orcid.org/0000-0002-9048-4840
Figures
Abstract
Brassaiopsis angustifolia K.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome of B. angustifolia was sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome of B. angustifolia is 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers of Brassaiopsis and Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of the Hydrocotyle group, Greater Raukaua group, Aralia-Panax group, and Asian Palmate group. The genus Brassaiopsis can be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny of B. angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genus Brassaiopsis.
Citation: Dong Z, Zhang R, Shi M, Song Y, Xin Y, Li F, et al. (2022) The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis. PLoS ONE 17(6): e0269819. https://doi.org/10.1371/journal.pone.0269819
Editor: Branislav T. Šiler, Institute for Biological Research, University of Belgrade, SERBIA
Received: January 18, 2022; Accepted: May 31, 2022; Published: June 30, 2022
Copyright: © 2022 Dong et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The assembled chloroplast genome and nuclear ribosomal ITS sequences have been uploaded to, and deposited in, GenBank as accession numbers OK638200 and OL352055, respectively.
Funding: This research was funded by the Economic Research Center of State Forestry and Grassland Administration of China (grand number: JYC2020-YN01).
Competing interests: The authors declare no conflict of interest.
Introduction
The genus Brassaiopsis Decne. & Planch. in the family Araliaceae includes nearly 45 species, with most of the species in the Himalayas, western China, Indochina, and the Malay Peninsula [1, 2], with southwestern China and northern Indochina as the main center of diversity [1]. The genus is part of the core Asian clade of Araliaceae [1, 3–5], and the species delimitation and infrageneric classification of Brassaiopsis has been highly controversial [1]. Brassaiopsis angustifolia K.M. Feng is an endangered shrub species. There is an urgent need to manage and conserve the natural resource of this shrub. However, information on its genetic and genomic background is limited. At present, the systematic position of B. angustifolia is not clear in the genus of Brassaiopsis. Therefore, knowledge of the genomics and phylogeny of its populations is essential to formulating effective protective measures.
During the past 20 years, molecular data have greatly improved our understanding of the phylogenetic relationships within the Araliaceae family and within the Apiales order [6]. Previous phylogenetic studies based on nuclear ribosomal DNA [1–5, 7–12] and chloroplast (cp) DNA [5, 7–13] sequence data have provided important clues about the evolution and diversity of Araliaceae plants. However, traditional phylogenies based on analysis of multiple genes have failed to well solve the relationship among species of Araliaceae. In addition, the early divergences of the Asian Palmate group have been clarified by using the chloroplast genome, but the backbone of its core is not totally resolved [14]. The family of Araliaceae, divided into four main clades by molecular systematics: Greater Rauakaua, Polyscias–Pseudopanax, Aralia–Panax, and Asian Palmate, respectively [3, 5, 10, 14]. Although several recent studies have made progress, sampling from Araliaceae has remained limited largely in most studies because of a focus on problems at other phylogenetic levels, individual geographic regions, or questions dedicated to a single genus [1, 2, 7, 8, 12]. The genus Brassaiopsis is part of the core Asian clade of Araliaceae. Based on the comprehensive analysis of internal transcribed spacer (ITS) and cp DNA data, the sister group relationship of Brassaiopsis and Trevesia were supported [1–3, 5, 7–11]. Because of low sequence quality, the few samples, and rapid divergence in early evolutionary history, the phylogenetic relationship among genera and species has not yet been well solved of Araliaceae [2–5, 9, 11, 15]. In addition, the species delimitation and infrageneric classification of Brassaiopsis are highly controversial. Therefore, it is necessary to use the existing cp genome data to construct a robust phylogenetic tree to clarify the phylogenetic relationships within Araliaceae.
In plants, the cp is the main locus of photosynthesis and carbon fixation [16, 17]. The cp genome of higher plants is a double-stranded circular DNA molecule ranging in size from 72 to 217 kb, containing about 130 genes. The cp genome has a typical tetrad structure, including a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeats (IRs) in most plants [17–19]. Compared with nuclear genomes, the uniqueness of the cp is evident in its maternal inheritance, small size, simple structure, and conserved sequences [20, 21]. The cp genome sequence reveals the phylogenetic relatedness visually at different taxonomic levels and provides an understanding of the evolution of a plant’s structure and function [22, 23]. Therefore, the genome sequence is widely used for cp inheritance, domestication studies, phylogeny, and adaptive evolution.
Here, we report for the first time, to our knowledge, the complete chloroplast genome sequence of B. angustifolia and characterize the structure, gene content, and organization of its genome. Then, we establish its codon usage frequencies, simple sequence repeats (SSRs), repeats, regions of high sequence divergence, nucleotide variability values, and the expansion and contraction of its IRs. Finally, we evaluated the phylogenetic position by comparative analysis based on 42 entire plastid genomes sequences of Araliaceae species and conducted a phylogenetic analysis of the Brassaiopsis genus using nuclear ribosomal ITS data. The results of this study can provide clues for species classification of Brassaiopsis and help to clarify the evolution and phylogenetic relationships of the species and genera of the Araliaceae family. Furthermore, this newly developed genomic resource will help further conserve the genetics of this endangered species.
Materials and methods
Sampling, DNA extraction and sequencing
We collected fresh and young leaves of B. angustifolia from a cultivated tree at the Southwest Forestry University, Kunming, China (102°45.489′ E, 25°3.639′ N). Total genomic DNA was extracted using the modified cetyltrimethylammonium bromide (CTAB) method [24]. Long-range polymerase chain reaction was performed following Zhang et al. [25], with 15 pairs of universal primers. The entire cp genome of B. angustifolia was sequenced via 250 bp paired-end sequencing on a HiSeq 2500 Platform (Illumina, Nanjing, China).
Analysis of cp genome assembly, annotation, and relative synonymous codon usage
Raw reads were filtered to remove low-quality reads, and de novo assembly of circular plastome and ITS sequence were carried out using GetOrganelle software [26]. We used Bandage software [27] to examine and screen the assembled cp genome of B. angustifolia. The cp genome was adjusted and annotated with Geneious software [28], and use the Organelle Genome DRAW software [29] to drawn a circular structure diagram of the entire genome. The entire annotated chloroplast genome and the ITS sequences were submitted to the National Center for Biotechnology Information (cp genome GenBank accession: OK638200; ITS GenBank accession: OL352055). Relative synonymous codon usage (RSCU) and codon usage were examined with CodonW (version 1.4.4) [30].
SSRs and identification of repeats
Using the MicroSatellite (MISA) identification tool [31], the minimum repeat number of mononucleotides was 10; for dinucleotides, it was five, and for trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeat motifs, it was four. The SSRs of 1–10 units of the nine complete cp genomes of the Asian Palmate group were detected. Complement repeats, forward repeats, palindromic repeats, and reverse repeats in non-SSR of the nine cp genomes were detected with the online software REPuter (https://bibiserv.cebitec.uni-bielefeld.de/reputer) [32], using the parameter default values. Tandem repeats in non-SSR of nine cp genomes were detected with online software TRF (http://tandem.bu.edu/trf/trf.basic.submit.html) [33].
Comparative genome analysis and sequence divergence
MAFFT software [34] was used to align the nine cp genomes of the Asian Palmate group, which were then manually adjusted with BioEdit software [35]. Sequence identity analysis was visualized with the mVISTA program in Shuffle-LAGAN mode [36], with the annotation for B. angustifolia as a reference. We performed a sliding-window analysis in the DnaSP software (version 6) [37] to evaluate the variability(π) of the plastomes. The window length was set to 600 bp and the step size to 200 bp. The contraction and expansion of the IR boundaries of nine species in the Asian Palmate group were visualized with the IRscope software [38].
Phylogenetic analysis based on cp genome and ITS data
Two different data matrices were assembled and analyzed using both maximum likelihood and Bayesian inference (BI) methods. Matrix I contained 42 taxa with complete plastid genomes available (S1 Table), including members of Aralia L. (5 spp.), Brassaiopsis Decne. & Planch. (2 spp.), Cheirodendron Nutt. ex Seem. (1 sp.), Chengiopanax C. B. Shang & J. Y. Huang (1 sp.), Dendropanax Decne. & Planch. (4 spp.), Eleutherococcus Maxim. (5 spp.), Fatsia Decne. & Planch. (2 spp.), Hedera L. (2 spp.), Heptapleurum Gaertn. (3 spp.), Heteropanax Seem. (1 sp.), Hydrocotyle L. (1 sp.), Kalopanax Miq. (1 sp.), Macropanax Miq. (1 sp.), Merrilliopanax H. L. Li (1 sp.), Oplopanax Miq. (1 sp.), Panax L. (6 spp.), Raukaua Seem. (3 spp.), Schefflera J. R. Forst. & G. Forst. (1 sp.), and Tetrapanax (K. Koch) K. Koch (1 sp.) (S1 Table). Angelica keiskei (Miq.) Koidz. (GenBank accession: MW125613), Diplopanax stachyanthus Hand.-Mazz. (GenBank accession: MG524991), Diplopanax stachyanthus Hand.-Mazz. (GenBank accession: KP318983), and Ostericum grosseserratum (Maxim.) Kitag. (GenBank accession: KT852844), were sampled as outgroups. Matrix II included 24 species of Brassaiopsis and eight species of Trevesia, and included 34 ITS sequences (S2 Table).
The complete cp genome and ITS matrix were aligned with MAFFT software (version 7) [34] and then manually edited with BioEdit 7.2.5 [35]. Bayesian inference was undertaken using MrBayes (version 3.2.6) [39]. Used jModelTest (version 2.1.10) [40] to select the most suitable replacement DNA model for phylogenetic reconstruction. The Markov chain Monte Carlo (MCMC) algorithm was run for 10,000,000 generations. The first 25% of the trees was discarded as aging trees and the remaining trees were used to generate a consensus tree for majority-rule. When the average standard deviation of split frequencies was less than 0.01, we considered the operation to be stable. Nodes with posterior probability (PP) values of 0.95 or greater were considered statistically significant. ML analysis was performed IQ-TREE (version 1.6.7) [41]. ML bootstrap support (BS) values of 70% or greater were considered well supported, and ML BS of less than 50% were considered poorly supported or unresolved. The best‐fit DNA substitution models for matrix I and matrix II, respectively, were chosen as “TPM1uf + I + G” (freqA = 0.3138, freqC = 0.1857, freqG = 0.1807, freqT = 0.3197, R (a) [AC] = 1.0000, R(b) [AG] = 1.6623, R(c) [AT] = 0.4054, R (d) [CG] = 0.4054, R(e) [CT] = 1.6623, R(f) [GT] = 1.0000, p-inv = 0.5260, and gamma shape = 0.9030) and “TrNef + G” (R(a) [AC] = 1.0000, R(b) [AG] = 4.0619, R (c) [AT] = 1.0000, R(d) [CG] = 1.0000, R(e) [CT] = 7.9724, R(f) [GT] = 1.0000, and gamma shape = 0.1830) to construct the phylogenetic tree. Results of all phylogenetic analysis are displayed with FigTree (version 1.4.3) (http://tree.bio.ed.ac.uk/publications/).
Results
Chloroplast genome characteristics of B. angustifolia
The size of the B. angustifolia cp genome was 156,534 bp, and exhibited the usual quadripartite structure, featuring a LSC region (86,509 bp), a SSC region (18,061 bp), and a pair of IRs (25,982 bp) (Fig 1). The guanine-cytosine (GC) content was 37.9% in whole cp, 36.1% and 31.9% in the LSC and SSC regions, respectively, whereas higher rates (43.0%) were distributed in the IR regions. A total of 133 genes were annotated in the sequenced B. angustifolia cp genome, containing 88 protein-coding genes, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs) (S3 Table). These genes belong to several categories with different functions; among which 17 duplicated genes were located in the IR regions, including six protein-coding genes (ndhB, rpl2, rpl23, rps7, ycf2, and ycf15), seven tRNAs (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and four rRNAs (rrn4.5S, rrn5S, rrn16S, and rrn23S). The transcription regulation of genes was believed to be affected by introns and exons. Nineteen genes (11 protein-coding genes and eight tRNAs) contained at least one intron, and three genes (clpP, ycf3, and rps12) had two introns (S3 Table).
Genes shown inside and outside of the circle are transcribed in clockwise and counterclockwise directions, respectively. Genes belonging to different functional groups are color‐coded. The GC and AT content are denoted by the dark gray and light gray colors in the inner circle, respectively.
According to the RSCU analysis (Fig 2), all protein-coding genes consisted of 21,582 codons. Among them, leucine (2,278 codons, 10.56%) was the most abundant amino acid, and isoleucine (1,824 codons, 8.45%) was the second. Each amino acid corresponded to at least one codon (tryptophan) and up to six (arginine, leucine, methionine, and serine). Trp had only one codon (UGG), which meant there was no codon usage bias. In addition, with the exception of methionine, most amino acids tended to use codons that ended in A/U rather than in C/G.
Bar diagram in different colors reflects codon usage bias (brown, yellow, purple, green, blue, and red, correspond to the proportion of different codons in descending order). Numbers represent codon quantities.
Analysis of SSR and repeats for the nine cp genomes of the Asian Palmate group
MISA analysis of 9 species cp genomic sequences from the Asian Palmate group revealed numerous SSR loci. In total, six types of SSRs (mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats) were detected based on the comparison of nine genomes in the Asian Palmate group. A total of 41 perfect SSRs were found in B. angustifolia (Fig 3A). Similarly, 38, 42, 37, 45, 42, 40, 46, and 35 SSRs were detected in Brassaiopsis hainla (Buch.-Ham.) Seem., Eleutherococcus brachypus Nakai, Eleutherococcus trifoliatus (L.) S. Y. Hu, Eleutherococcus gracilistylus (W. W. Sm.) S. Y. Hu, Eleutherococcus senticosus Maxim., Eleutherococcus sessiliflorus (Rupr. & Maxim.) S. Y. Hu, Kalopanax septemlobus Koidz., and Macropanax dispermus Kuntze. The most abundant type of SSR was mononucleotide repeats, which ranged from 17 bp in M. dispermus to 28 bp in E. gracilistylus, followed by dinucleotide, tetranucleotide, trinucleotide, pentanucleotide, and hexanucleotide repeats (Fig 3A). In the cp genome of B. angustifolia, most mononucleotide SSRs had A (47.83%) and T (34.78%) motifs, whereas all dinucleotide repeats were composed of TA (74.43%) and AT (28.57%) motifs (Fig 3B). Further analysis shows that most of the microsatellites were in the LSC region and a small proportion in the SSC and IR regions (Fig 3C). A total of 66 repeats were found in the B. angustifolia chloroplast genome, including tandem, palindromic, forward, inverted, and complement repeats. Similarly, 70, 75, 73, 70, 76, 78, 70, and 66 repeats were detected in B. hainla, E. brachypus, E. trifoliatus, E. gracilistylus, E. senticosus, E. sessiliflorus, K. septemlobus, and M. dispermus, respectively (Fig 3D).
(A) Number of six SSR types. (B) Number of identified SSR motifs of Brassaiopsis angustifolia. (C) Frequency of identified SSRs in large single copy (LSC) regions, small single copy (SSC) regions, and inverted repeat (IR) regions. (D) Total of four repeat types.
Identification of mutational hotspots among nine species of the Asian Palmate group
Sequence identity analysis was performed using mVISTA (Fig 4). Multiple sequence alignment revealed high similarity among the nine chloroplast genomes of the Asian Palmate group, which suggests that they are highly conserved; specifically, the results showed that the divergence of the single-copy (SC) region was larger than that of the IR region, and the divergence of the non-coding region was larger than that of the coding region.
The y-scale indicates identity from 50% to 100%. Gray arrows indicate the position and direction of each gene. Red indicates conserved non-coding sequences (CNSs). Blue indicates the exons of protein-coding genes (exon).
The software DnaSP 6.0 was used to calculate the nucleotide variation value (π) within 600 bp of the cp genome of B. angustifolia, B. hainla, E. brachypus, E. gracilistylus, E. senticosus, E. sessiliflorus, E. trifoliatus, K. septemlobus, and M. dispermus. The difference between the two Brassaiopsis species the value varied from 0 to 0.02333, with an average of 0.00395, suggesting that their genomic differences were small. However, five highly variable loci with much higher π values (π > 0.015), including the psbⅠ, petN-psbM-trnD-GUC, trnT-GUU-psbD, ndhF-rpl32, and ycf1, which were precisely located (Fig 5A). Among seven species of the Asian Palmate group and the two Brassaiopsis species, the π values varied from 0 to 0.02657 with a mean of 0.00461, indicating that the differences among species of the Asian Palmate group were larger than those between congeneric species. Five highly variable loci including the trnK-UUU-rps16, trnE-UUC-trnT-GGU, psbE-petL, ndhF, and ycf1 were precisely located in the nine species of the Asian Palmate group (π > 0.015; Fig 5B).
Comparison of the nucleotide variability (π) values of the two Brassaiopsis plastomes (A) and nine plastomes of the Asian Palmate group (B). (Window length, 600 bp, step size, 200 bp); x-axis: position of the midpoint of a window; y-axis: nucleotide diversity of each window.
Expansion and contraction of the inverted repeat regions
The IR boundaries of B. angustifolia and eight species of the Asian Palmate group were compared, and the possible expansion or contraction of IR regions was analyzed (Fig 6). The expansion and contraction of the boundaries of chloroplast genomic IR regions in nine plants of the Asian Palmate group were revealed, and the four junctions of two IRs between B. angustifolia and its related species were compared in detail (Fig 6). By comparing the plastids of the Asian Palmate group species, we found that the IR/LSC connections of IRb were mainly located between rpl2 and rps19 genes (Fig 6). In addition, the overlap of ycf1 genes appeared in different positions among the Asian Palmate group species, that is, the SSC region of B. angustifolia and the IRB/SSC junction of other seven species. M. dispermus did not contain the ycf1 gene. The ycf1 genes sited at the SSC/IRa boundary and the length of ycf1 ranged from 5,520 to 5,649 bp. The trnH genes of the four species in the Asian Palmate group were located in the LSC region, 2–5 bp away from the IRa-LSC border. In B. angustifolia, the expansion of the LSC region leads to the ndhF gene being at the IRb/LSC junction.
JLB, JSB, JSA, and JLA represent the junctions of LSC/IRb, IRb/SSC, SSC/IRa, and IRa/LSC, respectively. The Fig is not drawn to scale based on sequence length but shows only the relative change near or at the IR/SC junctions.
Phylogenetic relationships among the Araliaceae genera
In order to better understand the phylogenetic relationship among the 42 sequenced taxa from 19 genera of the Araliaceae, we have downloaded the corresponding sequences from GenBank (S1 Table). The BI and ML analysis of the complete plastid sequences of the main clades and most genera indicate that most phylogenetic relationships have a high degree of internal support (Fig 7). Araliaceae was divided into four groups: the Hydrocotyle group (BI-PP = 1.00, ML-BS = 100%), which included the Hydrocotyle. The Greater Raukaua Group (BI-PP = 0.9, ML-BS = 100%) included Schefflera, Cheirodendron, and Raukaua. The Aralia-Panax Group (BI-PP = 0.8, ML-BS = 98%) included Aralia and Panax. The Asian Palmate Group (BI‐PP = 0.7, ML-BS = 100%) can be divided into four small clades (A, B, C, and D). Clade A (BI‐PP = 0.7, ML-BS = 100%) included Oplopanax. Clade B (BI-PP = 0.9, ML-BS = 100%) included Heptapleurum, Heteropanax, and Tetrapanax. Clade C (BI‐PP = 1.00, ML-BS = 99%) included Chengiopanax plus Dendropanax. Clade D (BI-PP = 0.6, ML-BS = 92%) included Fatsia, Hedera, Merrilliopanax, Brassaiopsis, Eleutherococcus, Kalopanax, and Macropanax.
Numbers at each node are bootstrap support values. The tree is rooted in the plastome sequences of Angelica keiskei, Ostericum grosseserratum, and Diplopanax stachyanthus. Numbers associated with the branches are BI posterior probabilities (PP) and ML bootstrap value (BS), and asterisks (*) indicate BS/PP of 100/1.00.
Phylogenetic relationships among Brassaiopsis species
To better understand the phylogenetic relationships among Brassaiopsis species the ITS sequences of 24 Brassaiopsis species were used in the evaluation, with eight Trevesia species as the outgroup. The phylogenetic tree divided the genus into four main groups (Fig 8). Group Ⅰ (BI-PP = 1.00, ML-BS = 100%) included Brassaiopsis griffithii C. B. Clarke and Brassaiopsis simplicifolia C. B. Clarke. Group Ⅱ (BI-PP = 1.00, ML-BS = 94%) included Brassaiopsis elegans Ridl., Brassaiopsis malayana J. Wen & Frodin, ined., Brassaiopsis simplex (King) B. C. Stone, and Brassaiopsis sumatrana Ridl.. Group Ⅲ (BI-PP = 1.00, ML-BS = 95%) included Brassaiopsis ficifolia Dunn, Brassaiopsis grushvitzkyi J. Wen, Lowry & T. H. Nguyên, Brassaiopsis moumingensis (Y. R. Ling) C. B. Shang, Brassaiopsis phanrangensis C. B. Shang, Brassaiopsis producta (Dunn) C. B. Shang, and Brassaiopsis stellata K. M. Feng. Group Ⅳ (BI-PP = 0.66, ML-BS = 83%) included Brassaiopsis aculeata Seem., B. angustifolia, Brassaiopsis ciliata Dunn, Brassaiopsis ferruginea (H. L. Li) G. Hoo, Brassaiopsis glomerulata (Blume) Regel, Brassaiopsis gracilis Hand.-Mazz., B. hainla, Brassaiopsis hispida Seem., Brassaiopsis mitis C. B. Clarke, Brassaiopsis shweliensis W. W. Sm., and Brassaiopsis tripteris (H. Lév.) Rehder.
Numbers associated with the branches are BI posterior probabilities (PP) and ML bootstrap values (BS), and asterisks (*) indicate BS /PP of 100/1.00.
Discussion and conclusions
Comparison of cp genomes in the Asian Palmate group species
This study revealed the entire cp genome of an endangered shrub, namely B. angustifolia in the family Araliaceae. The plastome with a length of 156,534 bp was larger than the published plastome of B. hainla [13], which both possess the typical angiosperm quadripartite structure (Fig 1). The cp genomes are highly conserved for mostland plants. The difference in the size of the IRs and intergenic spacers leads to differences between the cp genomes [42]. Reportedly, the ycf1 and ycf2 genes are located on the border between the IR region and the LSC and SSC regions, and there is incomplete replication of these two genes [13, 43]. Unlike ycf2, the lengths of the truncated ycf1 genes were different among B. angustifolia, B. hainla, E. brachypus, E. gracilistylus, E. senticosus, E. sessiliflorus, E. trifoliatus, K. septemlobus, and M. dispermus (Fig 5). The gene ycf1 passes through the SSC-IRb region, and the truncated ycf1 gene was located in the LSC-IRa region. The change in length of the truncate ycf1 gene directly caused the shrinkage of the IR region in the plastomes of E. gracilistylus and K. septemlobus. In addition, in the M. dispermus, there is a truncated ycf1 gene in the LSC-IRa region; the same phenomenon exists in some species of other angiosperms [44]. Except for B. angustifolia, the ndhF gene is completely located in the SSC region in the other eight species, but the distance from the IRB/SSC boundary is different, which is consistent with the results obtained by Li et al. [13] in a study of seven species of Araliaceae.
Analysis of mutational hotspots
Not all genetic mutation events are random, with some clustering as hotspots [45, 46]. These mutation dynamics created highly variable regions in the genome [43]. In B. angustifolia and B. hainla plastomes, we identified five highly variable loci, which included psbⅠ, petN-psbM-trnD-GUC, trnT-GUU-psbD, ndhF-rpl32, and ycf1 (Fig 5A). In the Asian Palmate group, we identified five highly variable loci, which included trnK-UUU-rps16, trnE-UUC-trnT-GGU, psbE-petL, ndhF, and ycf1 (Fig 5B). Compared with other highly variable regions, ycf1 had the greatest genetic divergence among the nine sequenced plastid genomes of the Asian Palmate group (Fig 5B); from which, three highly variable loci were identified. These highly variable loci can be used for phylogenetic studies of the Araliaceae DNA barcode and at the species level. These results are partially congruent with those of Dong et al. [47] and Song et al. [48]. Therefore, Therefore, these associated regions can serve as barcodes as potential markers to reconstruct the phylogenetic relationship of Araliaceae.
The values of the nucleotide variability from the complete cp genomes among species of B. angustifolia and B. hainla were only 0.39%, and the nine species of the Asian Palmate group were 0.46%, which is similar to the nucleotide variability of two Panax L. species (0.40%) [49]; six Persea Mill., Machilus Nees, Phoebe Nees, and Cinnamomum Schaeff. species (0.32%) [50]; nine Lindera Thunb. species (0.48%) [51]; and 40 Populus L. species (0.36%) [52], which were much greater than the values of the two Phoebe Nees species (0.1%) [53], and three Alseodaphne Nees species (0.12%) [48], and were much less than the sequence divergence among the six Cymbidium Sw. species (3.70%) [54] and the five Epimedium L. species (3.97%) [55].
Phylogenetic analysis of Araliaceae and Brassaiopsis
Previous molecular markers provided limited information to elucidate the relationship among Araliaceae plants. Many studies have attempted to resolve the relationships within Araliaceae using molecular markers of ITS or plastid-region data, but the relationship of Araliaceae was still unclear [1–3, 5, 7–9, 11]. In addition, studies show that increased sampling of taxa can greatly improve overall phylogenetic accuracy [56–58]. Our study and Valcárcel et al. [14] had found that using the whole plastomes, with an appropriate sampling, can greatly aid the relationship between the deep pedigrees of the Araliaceae. The family of Araliaceae, grouped in four main clades in molecular phylogenies (Greater Rauakaua, Polyscias–Pseudopanax, Aralia–Panax, and Asian Palmate) [3, 5, 10, 14]. From the results of our study, four branches of phylogenetic meaningful have been identified in deep lineages of the Araliaceae. The topological backbone of the phylogenetic genome obtained in this work agrees with those previously published [5, 10, 14]. Moreover, the problems of several major branches of the Araliaceae were solved. In the Hydrocotyle group, the genus of Hydrocotyle is located within Araliaceae and is a relatively primitive genus (Fig 7). In the Greater Raukaua Group, our phylogenetic analysis revealed a sister group containing three Raukaua species, one Cheirodendron species, and the Schefflera digitata species (Fig 7), with strong support, as in the previously published phylogenetic tree constructed with combinations of plastid markers of trnL-trnF [5], trnD-trnT plus rpl16 [6], nuclear (ITS + external transcribed spacers [ETS]) plus plastid markers (ndhF-rpl32, rpl32-trnL, trnK-rps16, trnH-psbA) [7], and ITS plus plastid markers (ndhF, trnL–F, rps16, atpB–rbcL, rpl16 and psbA–trnH) [10]. In the Aralia-Panax Group, our phylogenetic analysis revealed that Aralia is nested among the members of Panax (Fig 7), which is consistent with the cp data from Nicolas et al. [6], Valcárcel et al. [9], Mitchell et al. [10], Plunkett et al. [11] and Li et al. [13], the nuclear ribosomal DNA data from Wen et al. [3], and the nuclear plus plastid data from Li et al. [8]. In the Asian Palmate Group, Oplopanax that appears as sister to the remaining Asian Palmate group, as found in previous studies [7, 10, 14]. Schefflera has been shown to be polyphyletic and distributed in the main pedigree of the family [7–11]. With the deepening of the research, there has been a large taxonomic rearrangement of Schefflera that resulted in the description of five new or reinstated genera [7, 59–64]. The resurrection of Heptapleurum in an Asian clade formerly belonging to Schefflera (Araliaceae), and with the completion of these transfers, Heptapleurum is now the largest genus in Araliaceae [63, 64]. In the Clade B, our phylogenomic analysis shows that sisterhood contained three Heptapleurum species and H. fragrans, Tetrapanax papyrifer (Hook.) K. Koch and Oplopanax horridus (Smith.) Miq. (Fig 7), likewise significant support in the nuclear ribosomal ITS sequences [2, 11], ITS plus plastid markers [9, 10], and the cp genomes data [14]. Furthermore, these clade can be divided into four groups, with strong support, the backbones of the phylogenomic topologies obtained here are consistent with previously published phylogenetic relationships [6, 10, 11, 14].
The phylogeny of Brassaiopsis was estimated based on ITS sequences. In the deep lineages of the Brassaiopsis species, four branches of phylogenetic importance have been identified. In group Ⅰ, B. griffithii and B. simplicifolia were located in the earliest-diverging extant lineage within Brassaiopsis (Fig 8). Four species B. elegans, B malayana, B. simplex, and B. sumatrana, were located within group Ⅱ (Fig 8). In group Ⅲ, B. ficifolia, B. grushvitzkyi, B. moumingensis, B. phanrangensis, B. producta, and B. stellata formed a sister relationship. In the study of Mitchell et al. [1], B. moumingensis was found to be a sister with B. grushvitzkyi, and B. stellata. In group Ⅳ, B. angustifolia was a sister with the other 11 Brassaiopsis species (Fig 8). In addition, our phylogeny supports the following relationships: the sisterhood of the B. hainla and B. aculeata, flowed B. glomerulata, as found in previous studies [1, 2]. Because of the limited mutation sites in the ITS sequence, the systematic relationship among Brassaiopsis species has not been solved, and needs to be studied further.
Supporting information
S3 Table. Annotated genes of the Brassaiopsis angustifolia cp genome.
https://doi.org/10.1371/journal.pone.0269819.s003
(DOCX)
References
- 1. Mitchell A, Wen J. Phylogeny of Brassaiopsis (Araliaceae) in Asia based on nuclear ITS and 5S-NTS DNA sequences. Syst. Bot. 2005;30(4):872–886.
- 2. Wen J, Zhu Y-P, Lee C, Widjaja E, Leng GS. Evolutionary relationships of Araliaceae in the Malesian region: a preliminary analysis. Acta Bot Yunnanica. 2008;30:391–399.
- 3. Wen J, Plunkett GM, Mitchell AD, Wagstaff SJ. The evolution of Araliaceae: A phylogenetic analysis based on ITS sequences of nuclear ribosomal DNA. Syst. Bot. 2001;26(1):144–167.
- 4. Mitchell A, Wen J. Phylogenetic utility and evidence for multiple copies of Granule-Bound Starch Synthase I (GBSSI) in Araliaceae. TAXON. 2004;53(1):29–44.
- 5. Plunkett G. M.; Wen J.; Lowry P. P. II Infrafamilial classifications and characters in Araliaceae: insights from the phylogenetic analysis of nuclear (ITS) and plastid (trnL-trnF) sequence data. Plant Syst. Evol. 2004;245:1–39.
- 6. Nicolas AN, Plunkett GM. The demise of subfamily Hydrocotyloideae (Apiaceae) and the re-alignment of its genera across the entire order Apiales. Mol Phylogenet Evol. 2009;53(1):134–151. pmid:19549570
- 7. Plunkett GM, Lowry PP, Fiaschi P, Frodin DG, Nicolas AN. Phylogeny, biogeography, and morphological evolution among and within the Neotropical and Asian clades of Schefflera (Araliaceae). TAXON. 2019;68(8): 1278–1313.
- 8. Li R, Wen J. Phylogeny and biogeography of Asian Schefflera (Araliaceae) based on nuclear and plastid DNA sequence data: Phylogeny and biogeography of Asian Schefflera. J. Syst. Evol. 2014;52(4):431–449.
- 9. Valcárcel V, Fiz-Palacios O, Wen J. The origin of the early differentiation of Ivies (Hedera L.) and the radiation of the Asian Palmate group (Araliaceae). Mol Phylogenet Evol. 2014;70: 492–503. pmid:24184542
- 10. Mitchell A, Li R, Brown JW, Schönberger I, Wen J. Ancient divergence and biogeography of Raukaua (Araliaceae) and close relatives in the southern hemisphere. Aust Syst Bot. 2012;25: 432.
- 11. Plunkett GM, Ii L, Frodin DG, Wen J. Phylogeny and geography of Schefflera: Pervasive polyphyly in the largest genus of Araliaceae. Ann Mo Bot Gard. 2005;92: 202–224.
- 12. Kim K, Nguyen VB, Dong JZ, Wang Y, Park JY, Lee S-C, et al. Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species. Sci. Rep. 2017;7(1):4917. pmid:28687778
- 13. Li R, Ma P-F, Wen J, Yi T-S. Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications. PLoS ONE. 2013;8(10):e78568. pmid:24205264
- 14. Valcárcel V, Wen J. Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae. J Syst Evol. 2019;57: 547–560.
- 15. Yi T, Lowry PP, Plunkett GM, Wen J. Chromosomal evolution in Araliaceae and close relatives. TAXON. 2004;53:987–1005.
- 16. Zhao YB, Yin JL, Guo HY, Zhang YY, Xiao W, Sun C, et al. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Front. Plant Sci. 2015;5:696. pmid:25642231
- 17. Daniell H, Lin C-S, Yu M, Chang W-J. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016;17:134. pmid:27339192
- 18. Bendich A.J. Circular chloroplast chromosomes: the grand illusion. Plant Cell. 2004;16(7):1661–1666. pmid:15235123
- 19. Sugiura M. The chloroplast genome. Plant Mol Biol. 1992;19:149–168. pmid:1600166
- 20. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci. 2005;102(23):8369–8374. pmid:15928076
- 21. Parks M, Cronn R, Liston A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 2009;7(1):84. pmid:19954512
- 22. Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci. 2007;104(49):19369–19374. pmid:18048330
- 23. Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci. 2010;107(10):4623–4628. pmid:20176954
- 24. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19(1):11–15.
- 25. Zhang T, Zeng C-X, Yang J-B, Li H-T, Li D-Z. Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs: universal primer pairs for sequencing whole chloroplast genomes and nuclear ribosomal DNAs. J. Syst. Evol. 2016;54(3):219–227.
- 26. Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, et al. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21:241, pmid:32912315
- 27. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: Interactive visualization of de novo genome assemblies. Bioinformatics. 2015;31(20):3350–3352, pmid:26099265
- 28. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–1649. pmid:22543367
- 29. Lohse M, Drechsel O, Kahlau S, Bock R. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013;41:W575–W581. pmid:23609545
- 30. Peden JF. Analysis of codon usage. Biosystems. 1999;5:45–50.
- 31. Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: A web server for microsatellite prediction. Bioinformatics. 2017;33(16):2583–2585. pmid:28398459
- 32. Kurtz S, Choudhuri JJ, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29(22):4633–4642. pmid:11713313
- 33. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. pmid:9862982
- 34. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780. pmid:23329690
- 35. Hall TA. BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp. Ser. 1999;41(41):95–98.
- 36. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32:W273–W279. pmid:15215394
- 37. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 2017;34(12):3299–3302. pmid:29029172
- 38. Amiryousefi A, Hyvönen J, Poczai P. IRscope: An online program to visualize the junction sites of chloroplast genomes. Hancock J, editor. Bioinformatics. 2018;34(17):3030–3031. pmid:29659705
- 39. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19(12):1572–1574. pmid:12912839
- 40. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9(8):772–772. pmid:22847109
- 41. Nguyen L-T, Schmidt HA, Haeseler A, Minh BQ. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015;32(1):268–274. pmid:25371430
- 42. Mardanov AV, Ravin NV, Kuznetsov BB, Samigullin TH, Antonov AS, Kolganova TV, et al. Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms. J. Mol. Evol. 2008;66(6):555–564. pmid:18463914
- 43. Song Y, Dong WP, Liu B, Xu C, Yao X, Gao J, et al. Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Front. Plant Sci. 2015;6:662. pmid:26379689
- 44. Wu ZH, Liao R, Yang TG, Dong X, Lan DQ, Qin R, et al. Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae). BMC Genomics 2020;21:621. pmid:32912155
- 45. Shaw J, Lickey EB, Schilling EE, Small RL. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot. 2007;94(3):275–288. pmid:21636401
- 46. Worberg A, Quandt D, Barniske A-M, Löhne C, Hilu KW, Borsch T. Phylogeny of basal eudicots: insights from non-coding and rapidly evolving DNA. Org. Divers. Evol. 2007;7(1):55–77.
- 47. Dong WP, Xu C, Li CH, Sun JH, Zuo YJ, Shi S, et al. ycf1, the most promising plastid DNA barcode of land plants. Sci. Rep. 2015;5(1):8348. pmid:25672218
- 48. Song Y, Yao X, Liu B, Tan YH, Corlett RT. Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae. Holzforschung. 2018;72(4):337–345.
- 49. Dong WP, Liu H, Xu C, Zuo YJ, Chen ZJ, Zhou SL. A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs. BMC Genet. 2014;15(1):138. pmid:25526752
- 50. Song Y, Yao X, Tan YH, Gan Y, Corlett RT. Complete chloroplast genome sequence of the avocado: gene organization, comparative analysis, and phylogenetic relationships with other Lauraceae. Can. J. For. Res. 2016;46(11):1293–1301.
- 51. Zhao M-L, Song Y, Ni J, Yao X, Tan YH, Xu Z-F. Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae). Sci. Rep. 2018;8(1):8844. pmid:29891996
- 52. Zong D, Gan PH, Zhou AP, Zhang Y, Zou XL, Duan AA, et al. Plastome sequences help to resolve deep-level relationships of Populus in the family Salicaceae. Front. Plant Sci. 2019;10:5. pmid:30723484
- 53. Song Y, Yao X, Tan YH. Gan Y, Yang J-B, Corlett RT. Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae). Tree Genet. Genomes. 2017, 13(6):120.
- 54. Yang J-B, Li D-Z, Li H-T. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour. 2014;14(5):1024–1031. pmid:24620934
- 55. Zhang YY, Du LW, Liu A, Chen JJ, Wu L, Hu WM, et al. The complete chloroplast genome sequences of five Epimedium species: lights into phylogenetic and taxonomic analyses. Front. Plant Sci. 2016, 7, 306. pmid:27014326
- 56. Dong ZH, Qu SH, Landrein S, Yu W-B, Xin J, Zhao WZ, et al. Increasing taxa sampling provides new insights on the phylogenetic relationship between Eriobotrya and Rhaphiolepis. Front Genet. 2022;13: 831206. pmid:35368713
- 57. Alvizu A, Eilertsen MH, Xavier JR, Rapp HT. Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea). Org Divers Evol. 2018;18: 279–290.
- 58. Pollock DD, Zwickl DJ, McGuire JA, Hillis DM. Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol. 2002;51: 664–671. pmid:12228008
- 59. Lowry PP II, Plunkett GM, Mora MM, Cano A, Fiaschi P, Frodin DG, et al. Studies in Neotropical Araliaceae. I. Resurrection of the genus Sciodaphyllum P. Browne to accommodate most New World species previously included in Schefflera J. R. Forst. & G. Forst. Brittonia. 2020;72: 1–15.
- 60. Lowry PP II, Plunkett GM, Neill DA. Studies in Neotropical Araliaceae. II. Resurrection of the Neotropical genus Crepinella for a clade of New World species previously included in Schefflera (Araliaceae). Novon. 2019;27: 253–261.
- 61. Fiaschi P, Lowry PP, Plunkett GM. Studies in Neotropical Araliaceae. III. Resurrection of the New World genus Didymopanax Decne. & Planch., previously included in Schefflera (Araliaceae). Brittonia. 2020;72: 16–22.
- 62. Plunkett GM, Lowry PP, Neill DA. Studies in Neotropical Araliaceae. VII. Two new genera, Cephalopanax and Frodinia, to accommodate the remaining species of Neotropical Schefflera. Brittonia. 2021;73: 251–261.
- 63. Lowry PP II, Plunkett GM. Resurrection of the Genus Heptapleurum for the Asian Clade of species previously included in Schefflera (Araliaceae). Novon. 2020;28: 143–170.
- 64. Esser H-J. Schefflera (Araliaceae) in Thailand becomes Heptapleurum. Thai For Bull Bot. 2021;49: 151–154.