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Article

Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae

by
Pingxuan Xie
1,†,
Lilei Tang
1,†,
Yanzhen Luo
1,
Changkun Liu
2 and
Hanjing Yan
1,3,*
1
College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
2
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
3
Key Laboratory of State Administration of Traditional Chinese Medicine for Production and Development of Cantonese Medicinal Materials, Guangzhou 510006, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Biology 2023, 12(2), 263; https://doi.org/10.3390/biology12020263
Submission received: 28 December 2022 / Revised: 21 January 2023 / Accepted: 26 January 2023 / Published: 7 February 2023
(This article belongs to the Special Issue Biodiversity, Phylogenomics and Innovation of Plant Germplasm Resources)
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Abstract

:

Simple Summary

The current classification of Plantaginaceae divides the family into 12 tribes. However, the inter-tribal relationships of this family remain unresolved, and phylogenetic and comparative studies on Plantaginaceae plastomes are also scarce. In this study, we compared 41 plastomes representing the 11 tribes of Plantaginaceae and uncovered the high conservation of the plastomes in terms of genome structure and gene content. Phylogenetic analyses based on 68 plastid protein-coding genes (PCGs) successfully elucidated the inter-tribal relationships of Plantaginaceae, especially disputed tribes, such as Plantagineae, Digitalideae, Veroniceae, Hemiphragmeae and Sibthorpieae. PhyParts analysis showed a certain extent of conflict between gene trees and species tree, revealing the limitations of phylogenetic analysis of Plantaginaceae using single or multiple plastid DNA sequences. Collectively, our results provide some basic information on the plastomes of the Plantaginaceae taxa and some new insights into the inter-tribal relationships of Plantaginaceae, laying the groundwork for future phylogenetic and taxonomic studies.

Abstract

Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.

1. Introduction

Plantaginaceae, a family of approximately 90 genera and 1900 species with great morphological diversity, includes annual or perennial herbs, sometimes shrubs (e.g., Veronica sect. Hebe, Aragoa), aquatics (e.g., Callitriche, Hippuris, etc.) or even carnivorous plants (e.g., Philcoxia) [1]. Many taxa (e.g., Plantago, Digitalis, Antirrhinum, etc.) have been widely explored and found to be of great medicinal, ornamental, and economic value. Since the clade “scroph Ⅱ” was discovered by Olmstead and Reeves [2], it has received considerable attention from researchers. Ultimately, a newly expanded clade now formally called Plantaginaceae, also accepted by APG IV [3], emerged from the former Scrophulariaceae due to the results of molecular phylogenetic studies [4,5,6,7,8,9,10]. According to the classification of Albach et al. [7], the enlarged Plantaginaceae contains 12 tribes (Plantagineae, Veroniceae, Digitalideae, Globularieae, Hemiphragmeae, Sibthorpieae, Russelieae, Cheloneae, Gratioleae, Antirrhineae, Callitricheae and Angelonieae) and each tribe was resolved as a well-supported monophyletic lineage [7,11,12,13,14].
Previous phylogenetic studies on Plantaginaceae were mainly based on single or multiple-locus DNA sequence data, such as nuclear ribosomal DNA internal-transcribed spacer (ITS), external-transcribed spacer (ETS), and plastid DNA ndhF, rbcL, trnL-trnF, rps16 intron and matK-trnK intron regions [7,11,12,15], providing some insights into phylogenetic relationships within Plantaginaceae. Nevertheless, these analyses failed to sort out the relationships among tribes well. For instance, the phylogenetic relationships among Plantagineae, Veroniceae, Digitalideae, Hemiphragmeae, Sibthorpieae, Cheloneae and Russelieae were unclear on account of weak support or even low resolution, which was shown in detail by Albach et al. [7] and systematically reviewed by Tank et al. [16]. Similar problems also arose in follow-up studies [10,11,12,13]. Additionally, incongruent topologies often appeared in Plantaginaceae phylogenetic trees, resulting in the phylogenetic positions of these tribes, such as Hemiphragmeae, Digitalideae, Plantagineae and Veroniceae, remaining ambiguous [7,11,12]. Specifically, there was an indication for a sister-group relationship of Hemiphragmeae and the clades of Digitalideae, Plantagineae and Veroniceae with strong support [7], whereas Hemiphragmeae was strongly supported as a sister to Veroniceae by Gormley et al. [12].
Recently, Mower et al. [17] suggested that Plantagineae may be more closely related to Digitalideae, while Veroniceae are related to Hemiphragmeae. The sister-group relationship of Plantagineae and Digitalideae was reproduced in their subsequent studies [14]. However, these studies mainly shed light on the relationships among genera in Plantagineae rather than tribes within Plantaginaceae. In addition, the taxon sampling of the tribes involved was also insufficient, thus still requiring in-depth analysis to uncover the phylogenetic relationships among these tribes. Overall, the limited taxon sampling and datasets consisting of single or a few DNA sequences may lead to an erroneous phylogenetic tree [18,19]. Therefore, to clarify the tribal-level phylogenetic relationships of Plantaginaceae, it is necessary to reconstruct a robust phylogeny based on a broad sampling and integration of more genes or genomic scale sequence data.
With the development of next-generation sequencing (NGS) technologies, plastid genomes (plastomes) have become more accessible. Owing to usually uniparental inheritance (in most case maternal inheritance), lack of recombination and moderate evolutionary rate [20,21], plastomes have been widely used for phylogenetic inferences [22,23,24]. In addition, structural variation, gene content and gene arrangement among plastomes can also serve as a supplement for phylogenetic inferences [25,26].
In this study, we newly sequenced the complete plastomes of six Plantaginaceae species and compared them with 35 publicly available plastomes of Plantaginaceae from GenBank. To investigate inter-tribal relationships in Plantaginaceae, a dataset of 43 species (41 Plantaginaceae species and two outgroup species) covering 11 tribes (except Globularieae) was constructed using 68 plastid protein-coding genes. Apart from concatenated analyses, we also undertook phylogenetic analysis using ASTRAL-III [27] as well as methods to assess the extent of conflict/concordance among plastid gene trees across the species tree [28]. The objectives of our study are to (1) investigate the structural and compositional variation of plastomes within Plantaginaceae; (2) reconstruct a robust phylogeny and preliminarily elucidate the relationships of the disputed tribes Plantagineae, Veroniceae, Digitalideae, Hemiphragmeae and Sibthorpieae; (3) assess the degree of gene-tree concordance and conflict within plastid data of Plantaginaceae, revealing the limitation of phylogenetic analyses using single or multiple plastid DNA sequences.

2. Materials and Methods

2.1. Plant Materials, DNA Extraction, Sequencing, Assembly and Annotation

A dataset of plastomes from 43 species was used in this study, representing 11 tribes of Plantaginaceae (except Globularieae). Among them, six species (Trapella sinensis, Adenosma glutinosum, Deinostema violacea, Ellisiophyllum pinnatum, Russelia equisetiformis and Linaria buriatica) were newly sequenced in this study. All voucher specimens were deposited in the Herbarium of Kunming Institute of Botany (KUN), Chinese Academy of Sciences. Voucher information, the source of material and GenBank accession numbers are given in Table S1. Pastomes of the other 37 species (including 2 outgroup taxa) were obtained from GenBank of the National Center for Biotechnology Information (NCBI) Table S2).
Genomic DNA of each sample was extracted from the silica gel-dried leaf tissues using the modified CTAB method [29]. Paired-end libraries with an average insert size of approximately 400 bp were prepared using a TruSeq DNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s instructions. 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 [30]. Clean paired-end (PE) reads were assembled using GetOrganelle v1.7.1 [31] with K-mer values of 21, 45, 65, 85, and 105 as seen using SPAdes v3.10 [32]. The complete plastome of Bacopa monnieri (MN736955) was set as the reference for Trapella sinensis, Adenosma glutinosum, and Deinostema violacea, while Antirrhinum majus (MW877560) was used for assembly the plastomes of Linaria buriatica, Russelia equisetiformis, and Ellisiophyllum pinnatum. Bandage v0.8.1 [33] was used to visualize and filter out the assembled contigs to generate a complete circular plastome. Plastid Genome Annotator [34] was used to annotate the newly assembled plastomes and then manually check the consistency of start/stop codons against the reference genome in Geneious v10.2.3 [35]. The tRNAscanSE web service [36] was used to confirm the tRNA genes with default parameters. Furthermore, the online program OrganellarGenomeDRAW (OGDRAW) [37] was used to draw circular plastome maps. GenBank accession numbers of the six plastomes generated in this study are presented in Table S1.

2.2. Plastome Comparative Analyses

To explore the structural variation of plastomes in Plantaginaceae, a set of 15 representative species was ultimately chosen, representing Plantagineae (Plantago fengdouensis, P. media, P. maritima, P. nubicola and Littorella uniflora), Veroniceae (Veronica persica), Digitalideae (Digitalis lanata), Hemiphragmeae (Hemiphragma heterophyllum), Sibthorpieae (Ellisiophyllum pinnatum), Callitricheae (Callitriche palustris), Russelieae (Russelia equisetiformis), Antirrhineae (Antirrhinum majus), Cheloneae (Penstemon rostriflorus), Gratioleae (Scoparia dulcis) and Angelonieae (Angelonia angustifolia). IR expansion/contraction of these plastomes was checked using IRscope [38]. After removing one copy of the IR region for each plastome, the general structural features were also analyzed with Mauve v2.3.1 [39].

2.3. Phylogenetic Analyses

Typically, organellar genomic regions are concatenated as a single locus to reconstruct phylogeny. However, a recent study uncovered notable levels of gene-tree conflict within the plastome [40], suggesting that concatenated analyses may be inappropriate for plastomes and should be performed with caution. In light of this, Gonçalves et al. [41] advocated for the use of both concatenation and multi-species coalescent methods (MSC) for inferring plastid phylogeny. Multispecies coalescent algorithms are divided into summary methods that use estimated gene trees to infer the species tree and “single-site” methods that use nucleotide alignments for species tree inference. Despite not performing full coalescent analysis, the summary method ASTRAL [27], used to estimate a species tree given a set of gene trees, has been shown to be statistically consistent under the multi-species coalescent model [42]. Therefore, we utilized both concatenated and ASTRAL analyses to infer phylogenetic relationships.
Before phylogenetic analyses, all 68 protein-coding genes (PCGs) were extracted from the plastomes of 43 taxa (Tables S1 and S2) using Geneious v10.2.3 [35]. Each protein-coding gene was separately aligned using MAFFT v7.450 [43] with the default settings and adjusted manually. Characteristics of alignments of 68 PCGs involved in the phylogenetic analyses are listed in Table S3. Scrophularia dentata and Buddleja sessilifolia (Scrophulariaceae: Lamiales) served as the outgroup according to the results of Gormley et al. [13].
For concatenated analysis, the multiple alignments of genes were concatenated into a 61,841 bp matrix (Table S3) with a preparation of a partition file generated by PhyloSuite v1.2.2 [44]. Maximum likelihood (ML) analyses were performed by IQ-TREE v2.1.2 [45] using UFBoot2 [46] with the most suitable partition models (Table S4) found by Modelfinder [47] with 1000 replicates. Besides, the SH-aLRT test [48] was used to assess branch supports. According to the Akaike information criterion (AIC), PartitionFinder v2.1.1 [49] was used to select the best-fit partitioning schemes and models for each gene with the default values (Table S5). Bayesian inference (BI), implemented in MrBayes v3.2.7a [50], was constructed with an average deviation of split frequencies below 0.01. Approximately 1000,000 generations were conducted for the matrix, and each set was sampled every 2500 generations with a burn-in of 25%. The software FigTree 1.4.4 (http://tree.bio.ed.ac.uk/software/Figtree/ (accessed on 1 September 2022)) was used to visualize the phylogenetic tree.
For the ASTRAL analysis, 68 plastid gene trees were inferred separately using RAxML v8.2.11 [51] with the GTRGAMMA model and 100 bootstrap replicates, and low-supported branches (<10% bootstrap support) in the gene trees were collapsed to improve species-tree inference [52]. Subsequently, the collapsed gene trees were imported into ASTRAL-III [27] with the default settings, which produced an estimated topology of the species tree with branch lengths and local posterior probabilities (LPP) as branch support values.
In addition, PhyParts [28] was used to examine how individual gene trees agree/conflict with the species tree by mapping the 68 plastid gene trees onto the species tree generated by ASTRAL analysis, with bootstrap support (BS) < 70% at gene-tree branches considered uninformative. A Python script by M. Johnson (https://github.com/mossmatters/phyloscripts/tree/master/phypartspiecharts (accessed on 20 October 2022)) was used to visualize the output of the PhyParts analyses. Pie charts on the species phylogeny show the number of gene trees that were concordant, conflicting, or uninformative concerning each node in the species tree.

3. Results

3.1. Features of the Plastomes

Illumina sequencing generated 6,069,200–30,408,958 paired-end clean reads for the six samples. Among them, 302,408–5,093,971 reads were mapped to the final assembly, with the average coverage ranging from 295.979× to 4,997.812× (Table S6). All newly sequenced plastomes were assembled into a typical quadripartite structure containing a large single copy (LSC) and a small single copy (SSC) separated by two inverted repeats (IRs, including IRa and IRb) (Figure 1).
By comparison, the size of the plastomes in Plantaginaceae ranged from 130,833 bp (Littorella uniflora) to 165,045 bp (Plantago asiatica) (Table 1), which identically consist of a pair of IRs (IRa and IRb, with lengths of 21,404–38,724 bp) separated by a LSC region (77,490–85,713 bp) and a SSC region (4577–18,447 bp) (Table 1). The total GC content ranged from 37.4% to 39.0%, with the lowest GC in Trapella sinensis and Limnophila sessiliflora and the highest GC content in Littorella uniflora (Table 1). Most plastomes contained the same 114 unique genes, including 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes (counting all duplicated genes only once) (Table 1, Table S7). Notably, the ycf15 gene is lost from the plastomes of Plantago, Littorella uniflora, Veronica polita, Veronica persica, Veronica eriogyne and Angelonia angustifolia. In addition, Littorella uniflora lacks functional copies of ndh genes (except ndhE); Angelonia angustifolia and Scoparia dulcis lack the infA gene, and a novel tRNA gene (trnL-CAG) is present in plastomes of Plantago maritima (Table S7).

3.2. Plastome Structural Variation

The IRs/LSC and IRs/SSC junctions among the plastomes of 15 diverse species representing 11 tribes in Plantaginaceae were compared to identify IR expansion/contraction. Overall, the boundaries of the LSC/IRb, IRb/SSC, SSC/IRa and IRa/LSC are relatively conservative within Plantaginaceae plastomes, with the rps19, ndhF, ycf1 and trnH genes located in the above junctions, respectively (Figure 2). The collinearity analysis also showed the conservation of plastome gene arrangement in most tribes (Figure 3). In contrast, three Plantago species, Plantago fengdouensis, P. media and P. maritima, have distinct IR expansions, as well as rearrangements, in the SSC and IRs, which leads to differences in the junction and gene arrangement (Figure 2 and Figure 3 and Figure S1). In addition, the size reduction in the LSC, SSC, and IRs of Littorella uniflora, especially the loss of ndh genes, brings about changes in the IRb/SSC junction (Figure 2).

3.3. Phylogenetic Analyses

Based on the concatenated dataset, both ML and BI phylogenies generated identical tree topologies, with nearly all nodes exhibiting high support values (ultrafast bootstrap (UFboot) = 100; SH-aLRT values (SH-aLRT) = 100; posterior probability (PP) = 1.00) (Figure 4), which recovered six distinct clades within Plantaginaceae: (Ⅰ) Gratioleae + Angelonieae (UFboot = 100; SH-aLRT = 100; PP = 1), (Ⅱ) Russelieae + Cheloneae (UFboot = 100; SH-aLRT = 100; PP = 1.00), (Ⅲ) Antirrhineae (UFboot = 100; SH-aLRT = 100; PP = 1.00), (Ⅳ) Callitricheae (UFboot = 100; SH-aLRT = 100; PP = 1.00), (Ⅴ) Sibthorpieae (UFboot = 100; SH-aLRT = 99.7; PP = 1.00), and (Ⅵ) Plantagineae + Digitalideae, Veroniceae + Hemiphragmeae (UFboot = 100; SH-aLRT = 100; PP = 1.00) (Figure 4). Among them, Gratioleae was clustered with Angelonieae at the base of the phylogenetic tree (Clade Ⅰ) sister to the rest of Plantaginaceae. Within the remaining tribes, Russelieae and Cheloneae formed the early diverging Clade Ⅱ, which was successively sister to Clade Ⅲ (Antirrhineae), Clade Ⅳ (Callitricheae), Clade Ⅴ (Sibthorpieae), and the Clade Ⅵ, in which Plantagineae was sister to Digitalideae (UFboot = 94; SH-aLRT = 95.3; PP = 1.00), while Veroniceae was supported as sister to Hemiphragmeae (UFboot = 100; SH-aLRT = 100; PP = 1.00).
Despite slight differences in some relationships observed within Veronica and Penstemon, the species tree topology implemented in ASTRAL was basically congruent with the result of the concatenation analyses, with high local posterior probability (LPP) values at most nodes (Figure 5). Notably, support values at the nodes of Digitalideae + Plantagineae (LPP = 0.7) and Russelieae + Cheloneae (LPP = 0.78) were relatively low, while the location of Sibthorpieae (LPP = 0.87) was only moderately supported.

3.4. Concordance and Conflict of the Gene Tree

PhyParts analyses revealed the numbers of consistent, conflicting, or uninformative gene trees for each node in the species tree, with a bootstrap support (BS) threshold of 70 set at nodes of each gene tree (Figure 6). From the pie chart, although a certain number of genes exhibited concordance, the majority of the plastid genes were largely uninformative for nodes of the phylogeny. Besides, there are gene-tree conflicts for nodes of the species tree of varying degrees. Notably, some nodes with the conflicting genes numbers close to or greater than the numbers of concordant genes seemed to have relatively low support in the species tree. The node of Digitalideae and Plantagineae exhibited more gene-tree conflict, with two concordant genes and five conflicting genes, while the node of Sibthorpieae had five concordant genes and ten conflicting genes. Besides, only five genes supported the sister relationship between Cheloneae and Russelieae, while thirteen genes conflicted with the topology (Figure 6).

4. Discussion

In general, the plastomes of Plantaginaceae are largely conserved in structure and gene content. Significant IR expansion and rearrangement of plastomes in Plantago were observed in three representative species including Plantago fengdouensis, P. media and P. maritima. Indeed, IR expansion and rearrangement of plastomes in Plantago have been discussed in detail by Mower et al. [17], and not discussed at length here. Furthermore, the absence of the ndh genes, ycf15 gene and infA gene found in Plantaginaceae appears to be common in angiosperms [53,54,55,56]. Gene loss can be the consequence of a sudden mutational event or the result of a slow process of accumulation of mutations during the pseudogenization that follows an initial loss-of-function mutation [57]. The loss of ndh genes only occurs in Littorella uniflora, which may be related to its amphibious lifestyle and partial reliance on Crassulacean acid metabolism (CAM) photosynthesis [17]. The ycf15 gene is lost in Plantago, Littorella uniflora, Veronica polita, V. persica, V. eriogyne and Angelonia angustifolia. Indeed, loss of the ycf15 gene has been observed in a variety of angiosperm lineages, which may have occurred independently throughout the evolution of angiosperms [54,58,59]. Angelonia angustifolia and Scoparia dulcis lack the infA gene and in many cases, the loss of the infA gene has been considered to be independently shifted to and expressed in the nucleus [55,60].
Given the weak support and conflicting topology in the phylogenetic tree, previous phylogenetic analyses based on single or several different plastid DNA sequences have failed to clarify the tribe-level relationships within Plantaginaceae [7,11,12,13], especially the phylogenetic placements of Russelieae, Cheloneae, Sibthorpieae, Digitalideae, Plantagineae, Veroniceae, and Hemiphragmeae. Indeed, the results of our concordance and conflict analysis verify these limitations. As shown in Figure 6, due to the lack of sufficient phylogenetic signal [40], most plastid genes are considered uninformative for nodes (BS < 70%) in species tree phylogeny. In addition, against a backdrop of largely uninformative genes, a few genes exhibit well-supported conflict at nodes to varying degrees, which can also correspond to the inter-tribal conflict in previous studies.
In most cases, systematic and stochastic error (presence of a non-phylogenetic signal in the data; the length of the genes) has been invoked by multiple studies to explain the potential source of conflict across the plastome [40,61,62,63]. Additionally, biparental inheritance and heteroplasmic recombination (both intra- and interspecific) have also been proposed as the potential source of biological conflict [40,64,65,66,67,68]. Here, we cannot conclude the causes of the well-supported conflict observed at nodes in our phylogeny based on the present limited analyses, which is also beyond the scope of this study. However, significantly, nodes with apparent conflicts require further research into the causes of conflict, particularly the possibility of biological conflict [40], which might help to understand the evolutionary history of plastomes of related taxa in Plantaginaceae. Moreover, the non-phylogenetic signals which can swamp the faint genuine phylogenetic signal presented in phylogeny also need to be appreciated [61,62].
In contrast, our phylogenomic analyses recovered the phylogenetic relationships of 11 tribes (except Globularieae) with robust support based on 68 plastid PCGs, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. On the whole, the phylogenetic positions of Gratioleae, Angelonieae, Russelieae, Cheloneae, Antirrhineae and Callitricheae are largely consistent with previous studies [7,8,10,11,12,13,14,15] and are strongly supported in our study. Therefore, the relationship between these tribes is not too controversial. Notably, the sister relationship between Russelieae and Cheloneae was recovered with robust support (UFboot = 100; SH-aLRT = 100; PP = 1.00), which was unprecedented in previous analyses [7,8,10,12,13,15]. Despite the substantial morphological differences between Russelieae and Cheloneae, pair-flowered Cymes (PFCs) were indicated as the common characteristic present in the ancestors of both tribes [69]. Wolfe et al. [15,70] also definitely argued that the cymose inflorescence of Russelieae–Cheloneae would be a synapomorphy of the two tribes.
The placement of Sibthorpieae was elusive in the phylogenetic tree based on different sequence data [7,13]. However, our plastid phylogenomic analyses showed that Sibthorpieae is more closely related to the clade of Plantagineae, Digitalideae, Veroniceae, and Hemiphragmeae with strong support (UFboot = 100; SH-aLRT = 99.7; PP = 1.00), which was not proposed by previous studies. Sibthorpieae comprises the two small genera Sibthorpia and Ellisiophyllum [7]. Floral morphology with four stamens, a five-lobed corolla, and a five-lobed calyx in Sibthorpieae (mainly in Ellisiophyllum) might show a little affinity with some species of its sister clade, particularly Hemiphragma and possibly Wulfenia of Veroniceae [71]. In addition, the morphological features of pollen grains of Sibthorpieae appear to be transitional. The types of exine sculptures of pollen grains in Sibthorpieae are not only common in most of the species in Russelieae, Cheloneae and Antirrhineae, but are also typical for Plantagineae and Veroniceae [13,72,73,74,75]. Chemically, although Sibthorpieae lacks iridoids and simple phenylethanoids widespread in Plantaginaceae, some of the caffeoyl phenylethanoid glycosides (GPGs) present in Sibthorpieae are similar to those found in Plantagineae, Digitalideae and Veroniceae [76]. Therefore, the placement of Sibthorpieae seems plausible in our study. Nonetheless, the new placement of Sibthorpieae should be treated with caution due to not sampling tribe Globularieae, which used to be related to a clade containing Plantagineae, Digitalideae, Veroniceae and Hemiphragmeae [7,8,11,13,77].
Plantagineae, Veroniceae, Digitaleae and Hemiphragmeae formed the Clade Ⅵ in our phylogenetic analyses. However, the inter-tribal relationships within this clade differed considerably between analyses. Both Olmstead et al. [77] and Bello et al. [8] recovered Digitalideae and Hemiphragmeae as successive sister groups to Veroniceae + Plantagineae with marginal support, whereas Albach et al. [7] found that the phylogenetic location of Digitalideae and Hemiphragmeae interchanged with moderate support. Moreover, Estes and Small [11] identified Digitalideae and Plantagineae as successive sister groups to Veroniceae + Hemiphragmeae, which was also supported by Gomley et al. [12], but the placement of Plantagineae was not well-supported in their studies. Unlike most previous studies, our analyses favor a sister-group relationship between Plantagineae and Digitalideae, and Veroniceae is closely allied to Hemiphragmeae. These affinities are also consistent with recent studies based on plastome, mitochondrial and nuclear ribosomal data [14,17].
Plantagineae was shown to be sister to Veroniceae in most molecular analyses [7,8,77,78], and their shared tetramerous flowers, seed morphology and some similar iridoid constituents between these two tribes were often discussed to show their affinities [7,78]. However, given that the pentamerous and zygomorphic flowers could be plesiomorphic in Plantaginaceae [79], the presence of tetramerous flowers in Plantagineae and Veroniceae was assumed to be an independent shift based on mixed evidence for fusion and loss of flower parts [5,71,78,79,80]. In addition, some similar phytochemical constituents in Plantagineae and Veroniceae seem to be more widespread in Plantaginaceae [77].
Plantagineae encompasses Plantago, Littorella and Aragoa [16], and the (nearly) actinomorphic, tetramerous corolla and the four equal stamens are considered synapomorphies for this tribe [7,78]. In contrast, Digitalideae, including Digitalis and Erinus, may retain a plesiomorphic character state with a shared long-tubed zygomorphic corolla with five lobes, a deeply five-lobed calyx, and four didynamous stamens (the fifth one is evident only in early ontogeny) [7,78]. Although there are few floral morphological commonalities between Plantagineae and Digitalideae, a similar seed morphology between Erinus and Plantagineae and a five-lobed calyx shared in Digitalideae and Aragoa might show their affinity [5,78]. Furthermore, similarities in chemosystematic characters could also help to understand their close relationship. Sorbitol, a carbohydrate with a limited distribution, appears to be the sugar characteristic for Digitalideae and Plantagineae, although Erinus contains glucose [76,81]. Indeed, the sorbitol found in Digitalis is also present in all species of Plantago [82] and Aragoa [83]. In contrast, mannitol was found to be the sugar characteristic of Veroniceae [76]. In addition, although Digitalis contains unique cardenolides and lacks iridoids, Erinus preserves the pattern of iridoid biosynthesis, retaining a phytochemical arsenal similar to that of related Plantagineae [76,81].
The sister relationship between Hemiphragmeae and Veroniceae was strongly supported in our analyses, which was also recovered by Gomley et al. [12] and Estes and Small [11], but it was rarely emphasized before. Hemiphragmeae merely contains a monotypic genus Hemiphragma from the Himalayas to China, Formosa, Philippines and Celebes with a fleshy, septicidal capsule, four stamens, an actinomorphic five-lobed corolla, a five-lobed calyx, and dimorphic leaves [1,71]. By comparison, Veroniceae with worldwide distribution comprises a large genus Veronica and the wulfenioid grade including Veronicastrum, Lagotis, Wulfenia, Picrorhiza, Wulfeniopsis and Paederota [6,7,16]. Almost all genera are characterized by two stamens (except Picrorhiza, which has four stamens). Veronica sensu lato is mainly characterized by (almost) actinomorphic flowers, a short to absent corolla tube, four-lobed corolla and four-lobed calyx, whereas the majority of genera in the wulfenioid grade have long-tubed zygomorphic flowers, a two-lipped corolla (commonly four corolla lobes) and five-lobed calyx (except Lagotis, variable in corolla and calyx number, and Wulfenia with a five-lobed corolla) [6]. Obviously, the floral morphological differences between Veroniceae and Hemiphragmeae are therefore unlikely enough to relate these two tribes. Nevertheless, their sister relationship can be justified by the following lines of evidence. First, Hemiphragmeae and Veroniceae share a common pollen type with similar patterns of sculpture of exine and aperture membranes [73]. Next, despite the differences in floral symmetry, the pentamerous calyx and corolla shared in Wulfenia and Hemiphragma might show a little affinity between the two tribes. Indeed, with several characteristics such as a two-lobed stigma, pentamerous calyx and corolla, divergent anther thecae, and colporate pollen, Wulfenia is frequently considered the most primitive representative in Veroniceae [6,84,85]. Furthermore, Wulfenia, Lagotis and Veronicastrum are supposed to be most likely to form the representatives of the early diverging branch of Veroniceae in most molecular studies [4,6,7], and some of the chemical compounds present in Wulfenia and Lagotis are very similar to those found in Hemiphragma [76]. Finally, based on comprehensive analyses [4,86,87], the possible common ancestral distribution area (the Qinghai-Tibetan Plateau (QTP) or Himalayan region) of the two tribes may also provide evidence for their sister relationships. Nonetheless, further studies are necessary to validate the relationships found here.

5. Conclusions

The present study enriches the genomic resources of the Plantaginaceae plastome and provides basic information on the plastome structure and gene content of Plantaginaceae taxa. Although Globularieae was not included in our analyses, the reconstructed robust plastome phylogeny, including 11 tribes of Plantaginaceae, provides some new insights into the inter-tribal relationships of Plantaginaceae. In addition, to further clarify the relationships between tribes in Plantaginaceae, future studies will benefit from using more extensive taxonomic sampling of all tribes from the plastid genome and employing more data from the nuclear and mitochondrial genomes.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/biology12020263/s1, Figure S1: Corresponding rearrangement areas of plastomes from Plantago fengdouensis, P. media and P. maritima were shown, with Plantago nubicola as the reference. Linear gene maps were drawn using OGDRAW (Greiner et al. 2019). The red line indicates the boundary where rearrangement begins. Genes are represented by boxes with genes above the line being transcribed right to left and those below the line transcribed left to right. For more detailed variations of plastome structure within Plantago, refer to Mower et al. (2021a); Figure S2: All 68 plastid gene trees using maximum likelihood (ML) method. Nodes <10% bootstrap support were collapsed;Table S1: list of six species newly sequenced with voucher and GenBank accession numbers; Table S2: list of Plastomes in phylogenetic analyses from GenBank; Table S3: characteristics of alignments of 68 PCGs involved in the phylogenetic analyses; Table S4: dataset partition with best-fitting models of molecular evolution (Modelfinder) for ML analyses; Table S5: dataset partition with the best-fitting model of molecular evolution (Partition Finder) for BI analyses; Table S6: summary of Illumina sequencing for six species; Table S7: list of genes identified in the plastomes of Plantaginaceae.

Author Contributions

Conceptualization, H.Y. and P.X.; data curation, P.X., L.T. and Y.L.; formal analysis, P.X., L.T. and Y.L.; writing—original draft, P.X. and L.T.; writing—review and editing, H.Y., C.L., P.X. and L.T.; supervision, H.Y. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Key-Area Research and Development Program of Guangdong Province, grant number 2021B0707010008.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The sequence data generated in this study are available in GenBank of the National Center for Biotechnology Information (NCBI) under the access numbers: OQ129603–OQ129608.

Acknowledgments

We are grateful to the Germplasm Bank of Wild Species at the Kunming Institute of Botany (KIB) and Molecular Biology Experiment Center, Germplasm Bank of Wild Species for facilitating this study, providing Adenosma glutinosum, Deinostema violacea, and Linaria buriatica plant materials. We also thank Naixing Shi (Yunnan Agricultural University) and Li Li (Northwest University) for providing valuable ideas for the analysis and the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Stevens, P.F. Angiosperm Phylogeny Website. Available online: http://www.mobot.org/MOBOT/research/APweb/ (accessed on 9 October 2022).
  2. Olmstead, R.G.; Reeves, P.A. Evidence for the Polyphyly of the Scrophulariaceae Based on Chloroplast RbcL and NdhF Sequences. Ann. Mo. Bot. Gard. 1995, 82, 176–193. [Google Scholar] [CrossRef]
  3. The Angiosperm Phylogeny Group. An Update of the Angiosperm Phylogeny Group Classification for the Orders and Families of Flowering Plants: APG IV. Bot. J. Linn. Soc. 2016, 181, 1–20. [Google Scholar] [CrossRef]
  4. Albach, D.C.; Chase, M.W. Incongruence in Veroniceae (Plantaginaceae): Evidence from Two Plastid and a Nuclear Ribosomal DNA Region. Mol. Phylogenet. Evol. 2004, 32, 183–197. [Google Scholar] [CrossRef]
  5. Albach, D.C.; Montserrat, M.; Fischer, M.A.; Chase, M.W. Evolution of Veroniceae: A Phylogenetic Perspective. Ann. Mo. Bot. Gard. 2001, 91, 275–302. [Google Scholar]
  6. Albach, D.C.; Martínez-Ortega, M.M.; Fischer, M.A.; Chase, M.W. A New Classification of the Tribe Veroniceae-Problems and a Possible Solution. TAXON 2004, 53, 429–452. [Google Scholar] [CrossRef]
  7. Albach, D.C.; Meudt, H.M.; Oxelman, B. Piecing Together the “New” Plantaginaceae. Am. J. Bot. 2005, 92, 297–315. [Google Scholar] [CrossRef]
  8. Bello, M.A.; Chase, M.W.; Olmstead, R.G.; Ronsted, N.; Albach, D. The Paramo Endemic Aragoa Is the Sister Genus of Plantago (Plantaginaceae; Lamiales): Evidence from Plastid RbcL and Nuclear Ribosomal ITS Sequence Data. Kew Bull. 2002, 57, 585. [Google Scholar] [CrossRef]
  9. Rahmanzadeh, R.; Müller, K.; Fischer, E.; Bartels, D.; Borsch, T. The Linderniaceae and Gratiolaceae Are Further Lineages Distinct from the Scrophulariaceae (Lamiales). Plant Biol. 2005, 7, 67–78. [Google Scholar] [CrossRef]
  10. Oxelman, B.; Kornhall, P.; Olmstead, R.G.; Bremer, B. Further Disintegration of Scrophulariaceae. TAXON 2005, 54, 411–425. [Google Scholar] [CrossRef]
  11. Estes, D.; Small, R.L. Phylogenetic Relationships of the Monotypic Genus Amphianthus (Plantaginaceae Tribe Gratioleae) Inferred from Chloroplast DNA Sequences. Syst. Bot. 2008, 33, 176–182. [Google Scholar] [CrossRef]
  12. Gormley, I.C.; Bedigian, D.; Olmstead, R.G. Phylogeny of Pedaliaceae and Martyniaceae and the Placement of Trapella in Plantaginaceae s. l. Syst. Bot. 2015, 40, 259–268. [Google Scholar] [CrossRef]
  13. Albach, D.C.; Tsymbalyuk, Z.M.; Mosyakin, S.L. Pollen Morphology of Ellisiophyllum and Sibthorpia (Plantaginaceae, Tribe Sibthorpieae) and Phylogenetics of the Tribe. Plant Syst. Evol. 2021, 307, 66. [Google Scholar] [CrossRef]
  14. Mower, J.P.; Hanley, L.; Wolff, K.; Pabón-Mora, N.; González, F. Complete Mitogenomes of Two Aragoa Species and Phylogeny of Plantagineae (Plantaginaceae, Lamiales) Using Mitochondrial Genes and the Nuclear Ribosomal RNA Repeat. Plants 2021, 10, 2673. [Google Scholar] [CrossRef]
  15. Wolfe, A.D.; Datwyler, S.L.; Randle, C.P. A Phylogenetic and Biogeographic Analysis of the Cheloneae (Scrophulariaceae) Based on ITS and MatK Sequence Data. Syst. Bot. 2002, 27, 138–148. [Google Scholar] [CrossRef]
  16. Tank, D.C.; Beardsley, P.M.; Kelchner, S.A.; Olmstead, R.G. Review of the Systematics of Scrophulariaceae s.l. and Their Current Disposition. Aust. Syst. Bot. 2006, 19, 289–307. [Google Scholar] [CrossRef]
  17. Mower, J.P.; Guo, W.; Partha, R.; Fan, W.; Levsen, N.; Wolff, K.; Nugent, J.M.; Pabón-Mora, N.; González, F. Plastomes from Tribe Plantagineae (Plantaginaceae) Reveal Infrageneric Structural Synapormorphies and Localized Hypermutation for Plantago and Functional Loss of Ndh Genes from Littorella. Mol. Phylogenet. Evol. 2021, 162, 107217. [Google Scholar] [CrossRef] [PubMed]
  18. Rokas, A.; Williams, B.L.; King, N.; Carroll, S.B. Genome-Scale Approaches to Resolving Incongruence in Molecular Phylogenies. Nature 2003, 425, 798–804. [Google Scholar] [CrossRef] [PubMed]
  19. Nabhan, A.R.; Sarkar, I.N. The Impact of Taxon Sampling on Phylogenetic Inference: A Review of Two Decades of Controversy. Brief. Bioinf. 2012, 13, 122–134. [Google Scholar] [CrossRef]
  20. Ravi, V.; Khurana, J.P.; Tyagi, A.K.; Khurana, P. An Update on Chloroplast Genomes. Plant Syst. Evol. 2008, 271, 101–122. [Google Scholar] [CrossRef]
  21. Jansen, R.K.; Ruhlman, T.A. Plastid Genomes of Seed Plants. In Genomics of Chloroplasts and Mitochondria; Bock, R., Knoop, V., Eds.; Springer: Dordrecht, The Netherlands, 2012; Volume 35, pp. 103–126. [Google Scholar]
  22. Jung, J.; Kim, C.; Kim, J.H. Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes. BMC Genomics 2021, 22, 231. [Google Scholar] [CrossRef]
  23. Ji, Y.; Liu, C.; Landis, J.B.; Deng, M.; Chen, J. Plastome Phylogenomics of Cephalotaxus (Cephalotaxaceae) and Allied Genera. Ann. Bot. 2021, 127, 697–708. [Google Scholar] [CrossRef] [PubMed]
  24. Zhao, F.; Chen, Y.P.; Salmaki, Y.; Drew, B.T.; Wilson, T.C.; Scheen, A.-C.; Celep, F.; Bräuchler, C.; Bendiksby, M.; Wang, Q.; et al. An Updated Tribal Classification of Lamiaceae Based on Plastome Phylogenomics. BMC Biol. 2021, 19, 2. [Google Scholar] [CrossRef] [PubMed]
  25. Mower, J.P.; Vickrey, T.L. Structural Diversity Among Plastid Genomes of Land Plants. Adv. Bot. Res. 2018, 85, 263–292. [Google Scholar] [CrossRef]
  26. Lyko, P.; Wicke, S. Genomic Reconfiguration in Parasitic Plants Involves Considerable Gene Losses alongside Global Genome Size Inflation and Gene Births. Plant Physiol. 2021, 186, 1412–1423. [Google Scholar] [CrossRef] [PubMed]
  27. Zhang, C.; Rabiee, M.; Sayyari, E.; Mirarab, S. ASTRAL-III: Polynomial Time Species Tree Reconstruction from Partially Resolved Gene Trees. BMC Bioinf. 2018, 19, 15–30. [Google Scholar] [CrossRef] [PubMed]
  28. Smith, S.A.; Moore, M.J.; Brown, J.W.; Yang, Y. Analysis of Phylogenomic Datasets Reveals Conflict, Concordance, and Gene Duplications with Examples from Animals and Plants. BMC Evol. Biol. 2015, 15, 150. [Google Scholar] [CrossRef] [PubMed]
  29. Doyle, J.J.; Doyle, J.L. A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochem. Bull. 1987, 19, 11–15. [Google Scholar]
  30. Chen, S.; Zhou, Y.; Chen, Y.; Gu, J. Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics 2018, 34, i884–i890. [Google Scholar] [CrossRef]
  31. Jin, J.J.; Yu, W.B.; Yang, J.B.; Song, Y.; dePamphilis, C.W.; Yi, T.S.; Li, D.Z. GetOrganelle: A Fast and Versatile Toolkit for Accurate de Novo Assembly of Organelle Genomes. Genome Biol. 2020, 21, 241. [Google Scholar] [CrossRef]
  32. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef]
  33. Wick, R.R.; Schultz, M.B.; Zobel, J.; Holt, K.E. Bandage: Interactive Visualization of de Novo Genome Assemblies. Bioinformatics 2015, 31, 3350–3352. [Google Scholar] [CrossRef]
  34. Qu, X.J.; Moore, M.J.; Li, D.Z.; Yi, T.S. PGA: A Software Package for Rapid, Accurate, and Flexible Batch Annotation of Plastomes. Plant Methods 2019, 15, 50. [Google Scholar] [CrossRef]
  35. Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al. Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data. Bioinformatics 2012, 28, 1647–1649. [Google Scholar] [CrossRef]
  36. Chan, P.P.; Lowe, T.M. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol. Biol. 2019, 1962, 1–14. [Google Scholar] [CrossRef]
  37. Greiner, S.; Lehwark, P.; Bock, R. OrganellarGenomeDRAW (OGDRAW) Version 1.3.1: Expanded Toolkit for the Graphical Visualization of Organellar Genomes. Nucleic Acids Res. 2019, 47, W59–W64. [Google Scholar] [CrossRef]
  38. Amiryousefi, A.; Hyvönen, J.; Poczai, P. IRscope: An Online Program to Visualize the Junction Sites of Chloroplast Genomes. Bioinformatics 2018, 34, 3030–3031. [Google Scholar] [CrossRef]
  39. Darling, A.C.E.; Mau, B.; Blattner, F.R.; Perna, N.T. Mauve: Multiple Alignment of Conserved Genomic Sequence with Rearrangements. Genome Res. 2004, 14, 1394–1403. [Google Scholar] [CrossRef]
  40. Walker, J.F.; Walker-Hale, N.; Vargas, O.M.; Larson, D.A.; Stull, G.W. Characterizing Gene Tree Conflict in Plastome-Inferred Phylogenies. PeerJ 2019, 7, e7747. [Google Scholar] [CrossRef]
  41. Gonçalves, D.J.P.; Simpson, B.B.; Ortiz, E.M.; Shimizu, G.H.; Jansen, R.K. Incongruence between Gene Trees and Species Trees and Phylogenetic Signal Variation in Plastid Genes. Mol. Phylogenet. Evol. 2019, 138, 219–232. [Google Scholar] [CrossRef]
  42. Mirarab, S.; Reaz, R.; Bayzid, M.S.; Zimmermann, T.; Swenson, M.S.; Warnow, T. ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation. Bioinformatics 2014, 30, i541–i548. [Google Scholar] [CrossRef]
  43. Katoh, K.; Standley, D.M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef]
  44. Zhang, D.; Gao, F.; Jakovlić, I.; Zou, H.; Zhang, J.; Li, W.X.; Wang, G.T. PhyloSuite: An Integrated and Scalable Desktop Platform for Streamlined Molecular Sequence Data Management and Evolutionary Phylogenetics Studies. Mol. Ecol. Resour. 2020, 20, 348–355. [Google Scholar] [CrossRef]
  45. Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef]
  46. Hoang, D.T.; Chernomor, O.; von Haeseler, A.; Minh, B.Q.; Vinh, L.S. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol. Biol. Evol. 2018, 35, 518–522. [Google Scholar] [CrossRef]
  47. Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef] [PubMed]
  48. Guindon, S.; Dufayard, J.F.; Lefort, V.; Anisimova, M.; Hordijk, W.; Gascuel, O. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Syst. Biol. 2010, 59, 307–321. [Google Scholar] [CrossRef]
  49. Lanfear, R.; Frandsen, P.B.; Wright, A.M.; Senfeld, T.; Calcott, B. PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol. Biol. Evol. 2016, 34, 772–773. [Google Scholar] [CrossRef]
  50. Ronquist, F.; Teslenko, M.; van der Mark, P.; Ayres, D.L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M.A.; Huelsenbeck, J.P. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst. Biol. 2012, 61, 539–542. [Google Scholar] [CrossRef]
  51. Stamatakis, A. RAxML version 8: A Tool for Phylogenetic Analysis and Post-analysis of Large Phylogenies. Bioinformatics 2014, 30, 1312–1313. [Google Scholar] [CrossRef]
  52. Zhang, C.; Sayyari, E.; Mirarab, S. ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. In Comparative Genomics; Meidanis, J., Nakhleh, L., Eds.; Springer: Cham, Switzerland, 2017; Volume 10562, pp. 53–75. [Google Scholar] [CrossRef]
  53. Silva, S.R.; Diaz, Y.C.A.; Penha, H.A.; Pinheiro, D.G.; Fernandes, C.C.; Miranda, V.F.O.; Michael, T.P.; Varani, A.M. The Chloroplast Genome of Utricularia Reniformis Sheds Light on the Evolution of the Ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PLoS ONE 2016, 11, e0165176. [Google Scholar] [CrossRef]
  54. Martínez-Alberola, F.; del Campo, E.M.; Lázaro-Gimeno, D.; Mezquita-Claramonte, S.; Molins, A.; Mateu-Andrés, I.; Pedrola-Monfort, J.; Casano, L.M.; Barreno, E. Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus Unedo Chloroplasts. PLoS ONE 2013, 8, e79685. [Google Scholar] [CrossRef]
  55. Millen, R.S.; Olmstead, R.G.; Adams, K.L.; Palmer, J.D.; Lao, N.T.; Heggie, L.; Kavanagh, T.A.; Hibberd, J.M.; Gray, J.C.; Morden, C.W.; et al. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 2001, 13, 645–658. [Google Scholar] [CrossRef]
  56. Braukmann, T.; Kuzmina, M.; Stefanović, S. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): Two clades within subgenus Grammica exhibit extensive gene loss. J. Exp. Bot. 2013, 64, 977–989. [Google Scholar] [CrossRef]
  57. Albalat, R.; Cañestro, C. Evolution by Gene Loss. Nat. Rev. Genet. 2016, 17, 379–391. [Google Scholar] [CrossRef]
  58. Jiao, Y.; Feng, G.; Huang, L.; Nie, G.; Li, Z.; Peng, Y.; Li, D.; Xiong, Y.; Hu, Z.; Zhang, X. Complete Chloroplast Genomes of 14 Subspecies of D. Glomerata: Phylogenetic and Comparative Genomic Analyses. Genes 2022, 13, 1621. [Google Scholar] [CrossRef]
  59. Liu, C.K.; Lei, J.Q.; Jiang, Q.P.; Zhou, S.-D.; He, X.J. The Complete Plastomes of Seven Peucedanum Plants: Comparative and Phylogenetic Analyses for the Peucedanum Genus. BMC Plant Biol. 2022, 22, 101. [Google Scholar] [CrossRef]
  60. Landau, A.; Diaz Paleo, A.; Civitillo, R.; Jaureguialzo, M.; Prina, A.R. Two InfA Gene Mutations Independently Originated from a Mutator Genotype in Barley. J. Hered. 2007, 98, 272–276. [Google Scholar] [CrossRef]
  61. Jeffroy, O.; Brinkmann, H.; Delsuc, F.; Philippe, H. Phylogenomics: The Beginning of Incongruence? Trends Genet. 2006, 22, 225–231. [Google Scholar] [CrossRef]
  62. Philippe, H.; Brinkmann, H.; Lavrov, D.V.; Littlewood, D.T.J.; Manuel, M.; Wörheide, G.; Baurain, D. Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. PLoS Biol. 2011, 9, e1000602. [Google Scholar] [CrossRef]
  63. Richards, E.J.; Brown, J.M.; Barley, A.J.; Chong, R.A.; Thomson, R.C. Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological? Syst. Biol. 2018, 67, 847–860. [Google Scholar] [CrossRef]
  64. Erixon, P.; Oxelman, B. Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast ClpP1 Gene. PLoS ONE 2008, 3, e1386. [Google Scholar] [CrossRef]
  65. Bouillé, M.; Senneville, S.; Bousquet, J. Discordant MtDNA and CpDNA Phylogenies Indicate Geographic Speciation and Reticulation as Driving Factors for the Diversification of the Genus Picea. Tree Genet. Genomes 2011, 7, 469–484. [Google Scholar] [CrossRef]
  66. D’Alelio, D.; Ruggiero, M.V. Interspecific Plastidial Recombination in the Diatom Genus Pseudo-Nitzschia. J. Phycol. 2015, 51, 1024–1028. [Google Scholar] [CrossRef]
  67. Walker, J.F.; Brown, J.W.; Smith, S.A. Analyzing Contentious Relationships and Outlier Genes in Phylogenomics. Syst. Biol. 2018, 67, 916–924. [Google Scholar] [CrossRef]
  68. Sancho, R.; Cantalapiedra, C.P.; López-Alvarez, D.; Gordon, S.P.; Vogel, J.P.; Catalán, P.; Contreras-Moreira, B. Comparative Plastome Genomics and Phylogenomics of Brachypodium: Flowering Time Signatures, Introgression and Recombination in Recently Diverged Ecotypes. New Phytol. 2018, 218, 1631–1644. [Google Scholar] [CrossRef] [PubMed]
  69. Weber, A. Pair-Flowered Cymes in the Lamiales: Structure, Distribution and Origin. Ann. Bot. 2013, 112, 1577–1595. [Google Scholar] [CrossRef]
  70. Wolfe, A.D.; Randle, C.P.; Datwyler, S.L.; Morawetz, J.J.; Arguedas, N.; Diaz, J. Phylogeny, Taxonomic Affinities, and Biogeography of Penstemon (Plantaginaceae) Based on ITS and CpDNA Sequence Data. Am. J. Bot. 2006, 93, 1699–1713. [Google Scholar] [CrossRef]
  71. Fischer, E. Scrophulariaceae. In Flowering Plants· Dicotyledons; Kadereit, J.W., Ed.; Springer: Berlin/Heidelberg, Germany, 2004; Volume 7, pp. 333–432. [Google Scholar]
  72. Tsymbalyuk, Z.M. Comparative palynomorphological investigation of the representatives of the tribe Antirrhineae Dumort. (Veronicaceae Durande). Mod. Phytomorphol. 2013, 3, 189–194. [Google Scholar] [CrossRef]
  73. Tsymbalyuk, Z.M. Palynomorphological Peculiarities of Representatives of the Order Lamiales s. l.: Phylogenetic Significance and Main Trends of Evolution. Presented at. Ph.D. Thesis, M.G. Kholodny Institute of Botany NAS of Ukraine, Kyiv, Ukraine, 2016. [Google Scholar] [CrossRef]
  74. Tsymbalyuk, Z.M.; Mosyakin, S.L. Atlas of Pollen Grains of Representatives of Plantaginaceae and Scrophulariaceae; M.G. Kholodny Institute of Botany, National Academy of Science of Ukraine: Kyiv, Ukraine, 2013; ISBN 978-966-02-7066-4. [Google Scholar] [CrossRef]
  75. Tsymbalyuk, Z.M.; Mosyakin, S.L. Evolutionary-palynomorphologycal analysis of some tribes of the family Plantaginaceae. Ukr. Bot. J. 2014, 71, 442–448. [Google Scholar] [CrossRef]
  76. Taskova, R.M.; Gotfredsen, C.H.; Jensen, S.R. Chemotaxonomy of Veroniceae and Its Allies in the Plantaginaceae. Phytochemistry 2006, 67, 286–301. [Google Scholar] [CrossRef]
  77. Olmstead, R.G.; Pamphilis, C.W.; Wolfe, A.D.; Young, N.D.; Elisons, W.J.; Reeves, P.A. Disintegration of the Scrophulariaceae. Am. J. Bot. 2001, 88, 348–361. [Google Scholar] [CrossRef] [PubMed]
  78. Bello, M.A.; Rudall, P.J.; González, F.; Fernández-Alonso, J.L. Floral Morphology and Development in Aragoa (Plantaginaceae) and Related Members of the Order Lamiales. Int. J. Plant Sci. 2004, 165, 723–738. [Google Scholar] [CrossRef]
  79. Schäferhoff, B.; Fleischmann, A.; Fischer, E.; Albach, D.C.; Borsch, T.; Heubl, G.; Müller, K.F. Towards Resolving Lamiales Relationships: Insights from Rapidly Evolving Chloroplast Sequences. BMC Evol. Biol. 2010, 10, 352. [Google Scholar] [CrossRef] [PubMed]
  80. Saunders, E.R. A study of Veronica from the viewpoint of certain floral characters. Bot. J. Linn. Soc. 1934, 49, 453–493. [Google Scholar] [CrossRef]
  81. Taskova, R.M.; Gotfredsen, C.H.; Jensen, S.R. Chemotaxonomic Markers in Digitalideae (Plantaginaceae). Phytochemistry 2005, 66, 1440–1447. [Google Scholar] [CrossRef]
  82. Rønsted, N.; Franzyk, H.; Mølgaard, P.; Jaroszewski, J.W.; Jensen, S.R. Chemotaxonomy and Evolution of Plantago L. Plant Syst. Evol. 2003, 242, 63–82. [Google Scholar] [CrossRef]
  83. Rønsted, N.; Bello, M.A.; Jensen, S.R. Aragoside and iridoid glucosides from Aragoa cundinamarcensis. Phytochemistry 2003, 64, 529–533. [Google Scholar] [CrossRef] [PubMed]
  84. Hong, D.Y. Taxonomy and evolution of the Veroniceae (Scrophulariaceae) with special reference to palynology. Opera Bot. 1984, 75, 5–60. [Google Scholar]
  85. Kampny, C.M.; Dengler, N.G. Evolution of flower shape in Veroniceae (Scrophulariaceae). Pl. Syst. Evol. 1997, 205, 1–25. [Google Scholar] [CrossRef]
  86. Li, G.D.; Kim, C.; Zha, H.G.; Zhou, Z.; Nie, Z.L.; Sun, H. Molecular Phylogeny and Biogeography of the Arctic-alpine Genus Lagotis (Plantaginaceae). TAXON 2014, 63, 103–115. [Google Scholar] [CrossRef]
  87. Surina, B.; Pfanzelt, S.; Einzmann, H.J.R.; Albach, D.C. Bridging the Alps and the Middle East: Evolution, Phylogeny and Systematics of the Genus Wulfenia (Plantaginaceae). TAXON 2014, 63, 843–858. [Google Scholar] [CrossRef]
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Figure 1. Circular maps of six Plantaginaceae plastomes. Genes shown outside of the outer layer circle are transcribed clockwise, whereas those insides are transcribed counterclockwise. The genes belonging to different functional groups are color-coded. The darker gray area of the inner circle denotes the GC content, while the lighter gray area indicates the AT content of the genome. LSC, large single-copy; SSC, small single-copy; IR, inverted repeat.
Figure 1. Circular maps of six Plantaginaceae plastomes. Genes shown outside of the outer layer circle are transcribed clockwise, whereas those insides are transcribed counterclockwise. The genes belonging to different functional groups are color-coded. The darker gray area of the inner circle denotes the GC content, while the lighter gray area indicates the AT content of the genome. LSC, large single-copy; SSC, small single-copy; IR, inverted repeat.
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Figure 2. Comparison of the borders of the LSC, SSC, and IR regions of the plastomes from 15 representative species of Plantaginaceae. JLB: junction line between LSC and IRb; JSB: junction line between IRb and SSC; JSA: junction line between SSC and IRa; JLA: junction line between IRa and LSC.
Figure 2. Comparison of the borders of the LSC, SSC, and IR regions of the plastomes from 15 representative species of Plantaginaceae. JLB: junction line between LSC and IRb; JSB: junction line between IRb and SSC; JSA: junction line between SSC and IRa; JLA: junction line between IRa and LSC.
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Figure 3. Comparison of plastomes from 15 representative species of Plantaginaceae using the MAUVE algorithm. Rectangular blocks of the same color indicate collinear regions of sequences and the histograms within each block indicate the degree of sequence similarity. The pink blocks indicate the IR regions. The red frame indicates the areas of structural rearrangement, including translocations and inversions (see Figure S1 for more details).
Figure 3. Comparison of plastomes from 15 representative species of Plantaginaceae using the MAUVE algorithm. Rectangular blocks of the same color indicate collinear regions of sequences and the histograms within each block indicate the degree of sequence similarity. The pink blocks indicate the IR regions. The red frame indicates the areas of structural rearrangement, including translocations and inversions (see Figure S1 for more details).
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Figure 4. Phylogeny of Plantaginaceae reconstructed by analyses of 68 concatenated plastid PCGs using maximum likelihood (ML) and Bayesian inference (BI) methods. Values at nodes represent the ultrafast bootstrap support values (UFBoot) and SH-aLRT values (SH-aLRT) of the maximum likelihood analysis and the posterior probabilities (PP) of the BI analysis values. All unlabeled nodes indicate high support values (UFBoot = 100; SH-aLRT = 100; PP = 1.00).
Figure 4. Phylogeny of Plantaginaceae reconstructed by analyses of 68 concatenated plastid PCGs using maximum likelihood (ML) and Bayesian inference (BI) methods. Values at nodes represent the ultrafast bootstrap support values (UFBoot) and SH-aLRT values (SH-aLRT) of the maximum likelihood analysis and the posterior probabilities (PP) of the BI analysis values. All unlabeled nodes indicate high support values (UFBoot = 100; SH-aLRT = 100; PP = 1.00).
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Figure 5. Species tree of Plantaginaceae reconstructed by ASTRAL based on 68 plastid protein-coding genes. Values at nodes represent local posterior probabilities (LPP) and all unlabeled nodes indicate high support values (LPP = 1.00). All 68 plastid gene trees of Plantaginaceae were shown in Figure S2.
Figure 5. Species tree of Plantaginaceae reconstructed by ASTRAL based on 68 plastid protein-coding genes. Values at nodes represent local posterior probabilities (LPP) and all unlabeled nodes indicate high support values (LPP = 1.00). All 68 plastid gene trees of Plantaginaceae were shown in Figure S2.
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Figure 6. Summary of gene-tree concordance and conflict based on the PhyParts analysis of the 68 plastid gene trees mapped against the species tree (ASTRAL). The pie charts show the proportion and the numbers of genes in concordance (blue), conflict (green = a single dominant alternative; red = all other conflicting trees), and without information (grey) at each node in the species tree.
Figure 6. Summary of gene-tree concordance and conflict based on the PhyParts analysis of the 68 plastid gene trees mapped against the species tree (ASTRAL). The pie charts show the proportion and the numbers of genes in concordance (blue), conflict (green = a single dominant alternative; red = all other conflicting trees), and without information (grey) at each node in the species tree.
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Table
Table 1. Comparison of plastome features among Plantaginaceae plants.
Table 1. Comparison of plastome features among Plantaginaceae plants.
TribesSpeciesGC
Content (%)		Size (bp)Gene Number (Unique)
GenomeLSCIRSSCTotalPCGsrRNAtRNA
AngelonieaeAngelonia angustifolia37.7154,31684,11027,12815,95011278430
AntirrhineaeAntirrhinum majus37.9152,60683,20525,73417,93311480430
Linaria buriatica37.8150,66581,76625,64817,60311480430
CallitricheaeCallitriche palustris37.8150,13881,43225,66717,37211480430
Hippuris vulgaris37.6152,76382,98325,74318,29411480430
CheloneaePenstemon cyaneus37.9152,60483,72425,53417,81211480430
Penstemon fruticosus37.9152,70483,68425,59917,82211480430
Penstemon personatus37.9152,60283,72825,52817,81811480430
Penstemon rostriflorus37.9152,59883,65125,56417,81911480430
DigitalideaeDigitalis lanata38.6153,10883,93625,74317,68611480430
GratioleaeDeinostema violacea37.5154,28085,71325,17918,20911480430
Adenosma glutinosum37.5154,22084,82025,63618,12811480430
Bacopa monnieri37.6152,49583,76525,66817,39411480430
Limnophila sessiliflora37.4152,39583,16325,54518,14211480430
Scoparia dulcis37.5153,70185,02925,27318,12611379430
Trapella sinensis37.4152,29783,83025,01018,44711480430
HemiphragmeaeHemiphragma heterophyllum38.1152,70783,26825,80817,82311480430
PlantagineaeLittorella uniflora39.0130,83377,49021,40410,53510369430
Aragoa cleefii38.3150,28581,86525,34717,72611379430
Aragoa abietina38.2150,32081,89925,34717,72711379430
Plantago lagopus38.3150,08882,57424,54218,43011379430
Plantago nubicola38.2151,61183,65724,95518,04411379430
Plantago maritima38.6158,35882,22333,735866511479431
Plantago aristata38.4149,9108245024,58218,29611379430
Plantago media38.0164,13082,75738,398457711379430
Plantago depressa38.0164,61782,93338,388490811379430
Plantago fengdouensis38.0164,97682,97238,644471611379430
Plantago asiatica38.1165,04582,96438,724463311379430
RusselieaeRusselia equisetiformis38.2153,33783,84425,73818,01711480430
SibthorpieaeEllisiophyllum pinnatum38.2152,42483,23225,78717,61811480430
VeroniceaeVeronica polita37.9150,19181,84725,46517,41411379430
Veronica persica37.9150,19881,85025,46517,41811379430
Veronica eriogyne38.0151,08382,30225,66617,44911379430
Veronica undulata38.1151,17882,64425,56617,40211480430
Veronica ovata38.0152,24983,18725,67917,70411480430
Veronica nakaiana37.9152,31983,19525,71117,70211480430
Picrorhiza scrophulariiflora38.1152,64383,19125,82917,79411480430
Veronicastrum axillare38.3152,69183,55925,76517,60211480430
Veronicastrum sibiricum38.3152,93083,61625,75717,80011480430
Lagotis brevituba38.3152,96783,74025,69117,84511480430
Lagotis yunnanensis38.4152,97983,64125,67717,79411480430
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Xie, P.; Tang, L.; Luo, Y.; Liu, C.; Yan, H. Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae. Biology 2023, 12, 263. https://doi.org/10.3390/biology12020263

AMA Style

Xie P, Tang L, Luo Y, Liu C, Yan H. Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae. Biology. 2023; 12(2):263. https://doi.org/10.3390/biology12020263

Chicago/Turabian Style

Xie, Pingxuan, Lilei Tang, Yanzhen Luo, Changkun Liu, and Hanjing Yan. 2023. "Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae" Biology 12, no. 2: 263. https://doi.org/10.3390/biology12020263

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