Abundant incongruence in a clade endemic to a biodiversity hotspot: Phylogenetics of the scrub mint clade (Lamiaceae)

The Scrub Mint clade(Lamiaceae) provides a unique system for investigating the evolutionary processes driving diversification in the North American Coastal Plain from both a systematic and biogeographic context. The clade comprisesDicerandra, Conradina, Piloblephis, Stachydeoma, and four species of the broadly defined genus Clinopodium(Mentheae; Lamiaceae), almost all of which are endemic to the North American Eastern Coastal Plain. Most species of this clade are threatened or endangered and restricted to sandhill or a mosaic of scrub habitats. We analyzed relationships in this clade to understand the evolution of the group and identify evolutionary mechanisms acting on the clade, with important implications for conservation. We used a target-capture method to sequence and analyze 238 nuclear loci across all species of scrub mints, reconstructed the phylogeny, and calculated gene tree concordance, gene tree estimation error, and reticulation indices for every node in the tree using ML methods. Phylogenetic networks were used to determine reticulation events. Our nuclear phylogenetic estimates were consistent with previous results, while greatly increasing the robustness of taxon sampling. The phylogeny resolved the full relationship between Dicerandra and Conradina and the less-studied members of the clade (Piloblephis, Stachydeoma, Clinopodium spp.). We found hotspots of gene tree discordance and reticulation throughout the tree, especially in perennial Dicerandra. Several instances of reticulation events were uncovered between annual and perennial Dicerandra, and within the Conradina + allies clade. Incomplete lineage sorting also likely contributed to phylogenetic discordance. These results clarify phylogenetic relationships in the clade and provide insight on important evolutionary drivers in the clade, such as hybridization. General relationships in the group were confirmed, while the large amount of gene tree discordance is likely due to reticulation across the phylogeny.

[Identification and analysis of terpene synthase (TPS) gene family in Schizonepeta tenuifolia]

Terpenoids are important secondary metabolites of plants that possess both pharmacological activity and economic value. Terpene synthases(TPSs) are key enzymes in the synthesis process of terpenoids. In order to investigate the TPS gene family members and their potential functions in Schizonepeta tenuifolia, this study conducted a systematic analysis of the TPS gene family of S. tenuifolia based on the whole genome data of S. tenuifolia using bioinformatics methods. The results revealed 57 StTPS members identified from the genome database of S. tenuifolia. The StTPS family members encoded 285-819 amino acids, with protein molecular weights ranging from 32.75 to 94.11 kDa, all of which were hydrophilic proteins. The StTPS family members were mainly distributed in the cytoplasm and chloroplasts, exhibiting a random and uneven physical localization pattern. Phylogenetic analysis showed that the StTPS genes family were divided into six subgroups, mainly belonging to the TPS-a and TPS-b subfamilies. Promoter analysis predicted that the TPS gene family members could respond to various stressors such as light, abscisic acid, and methyl jasmonate(MeJA). Transcriptome data analysis revealed that most of the TPS genes were expressed in the roots of S. tenuifolia, and qRT-PCR analysis was conducted on genes with high expression in leaves and low expression in roots. Through the analysis of the TPS gene family of S. tenuifolia, this study identified StTPS5, StTPS18, StTPS32, and StTPS45 as potential genes involved in sesquiterpene synthesis of S. tenuifolia. StTPS45 was cloned for the construction of an prokaryotic expression vector, providing a reference for further investigation of the function and role of the TPS gene family in sesquiterpene synthesis.

Full-length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba

Glechoma longituba has been frequently used in treating urolithiasis and cholelithiasis due to the presence of flavonoids, which are its major bioactive constituents. However, research on the molecular background of flavonoid biosynthesis in G. longituba is limited. In this study, we used single-molecule real-time combined with next-generation sequencing technologies to construct the complete transcriptome of G. longituba. We identified 404,648 non-redundant transcripts, including 249,697 coding sequences, 197,811 simple sequence repeats, 174,846 long noncoding RNA, and 176,554 coding RNA. Moreover, we functionally annotated 346,218 isoforms (85.56%) and identified 86,528 differentially expressed genes. We also identified 55 non-redundant full-length isoforms related to the flavonoid biosynthetic pathway. Pearson correlation analysis revealed that the expression levels of some key genes of the flavonoid biosynthesis pathway were significantly positively correlated with the flavonoid metabolites. Furthermore, we performed bioinformatics analysis (sequence and structural) of isoform_47029 (encoding flavanone 3-hydroxylase) and isoform_53692 (encoding flavonol synthase) to evaluate their potential biological functions. Finally, we validated gene expression levels of 12 flavonoid-related key enzyme genes using quantitative real-time PCR. Overall, this study provides full-length transcriptome information on G. longituba for the first time and valuable molecular resources for further research on the medicinal properties of this plant.

Reassessing the genetic variability of Tectona grandis through high-throughput genotyping: Insights on its narrow genetic base

Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its first sources of diversity and little is known about the genetic origin and genetic variability. Thus, this study aimed to investigate the genetic diversity and genetic population structure existing in a representative teak germplasm bank collection. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 3 giga bases per sample, the sequences are aligned using the genome, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four populations with considerable genetic variability between and within them. While the genetic variability in teak is generally known to be narrow, this study confirmed the presence of genetic variability scale in teak, which is contrary to what was initially expected.

Comparative Analysis of Plastomes in Elsholtzieae: Phylogenetic Relationships and Potential Molecular Markers

The Elsholtzieae, comprising ca. 7 genera and 70 species, is a small tribe of Lamiaceae (mint family). Members of Elsholtzieae are of high medicinal, aromatic, culinary, and ornamentals value. Despite the rich diversity and value of Elsholtzieae, few molecular markers or plastomes are available for phylogenetics. In the present study, we employed high-throughput sequencing to assemble two Mosla plastomes, M. dianthera and M. scabra, for the first time, and compared with other plastomes of Elsholtzieae. The plastomes of Elsholtzieae exhibited a quadripartite structure, ranging in size from 148,288 bp to 152,602 bp. Excepting the absence of the pseudogene rps19 in Elsholtzia densa, the exhaustive tally revealed the presence of 132 genes (113 unique genes). Among these, 85 protein-coding genes (CDS), 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1) were annotated. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. Notably, the E. eriostchya plastid genome exhibited increased GC content regions in the LSC and SSC, resulting in an increased overall GC content of the entire plastid genome. The E. densa plastid genome displayed modified boundaries due to inverted repeat (IR) contraction. The sequences of CDS and intergenic regions (IGS) with elevated variability were identified as potential molecular markers for taxonomic inquiries within Elsholtzieae. Phylogenetic analysis indicated that four genera formed monophyletic entities, with Mosla and Perilla forming a sister clade. This clade was, in turn, sister to Collinsonia, collectively forming a sister group to Elsholtzia. Both CDS, and CDS + IGS could construct a phylogenetic tree with stronger support. These findings facilitate species identification and DNA barcoding investigations in Elsholtzieae and provide a foundation for further exploration and resource utilization within this tribe.

East Asian-North American disjunctions and phylogenetic relationships within subtribe Nepetinae (Lamiaceae)

Biogeographic disjunctions, including intercontinental disjunctions, are frequent across plant lineages and have been of considerable interest to biologists for centuries. Their study has been reinvigorated by molecular dating and associated comparative methods. One of the "classic" disjunction patterns is that between Eastern Asia and North America. It has been speculated that this pattern is the result of vicariance following the sundering of a widespread Acrto-Teritary flora. Subtribe Nepetinae in the mint family (Lamiaceae) is noteworthy because it contains three genera with this disjunction pattern: Agastache, Dracocephalum, and Meehania. These disjunctions are ostensibly the result of three separate events, allowing for concurrent testing of the tempo, origin, and type of each biogeographic event. Using four plastid and four nuclear markers, we estimated divergence times and analyzed the historical biogeography of Nepetinae, including comprehensive sampling of all major clades for the first time. We recover a well-supported and largely congruent phylogeny of Nepetinae between genomic compartments, although several cases of cyto-nuclear discordance are evident. We demonstrate that the three disjunctions are pseudo-congruent, with unidirectional movement from East Asia at slightly staggered times during the late Miocene and early Pliocene. With the possible exception of Meehania, we find that vicariance is likely the underlying driver of these disjunctions. The biogeographic history of Meehania in North America may be best explained by long-distance dispersal, but a more complete picture awaits deeper sampling of the nuclear genome and more advanced biogeographical models.

The First Genome-Wide Mildew Locus O Genes Characterization in the Lamiaceae Plant Family

Powdery mildew (PM) is a widespread plant disease that causes significant economic losses in thousands crops of temperate climates, including Lamiaceae species. Multiple scientific studies describe a peculiar form of PM-resistance associated at the inactivation of specific members of the Mildew Locus O (MLO) gene family, referred to as mlo-resistance. The characterization of Lamiaceae MLO genes, at the genomic level, would be a first step toward their potential use in breeding programs. We carried out a genome-wide characterization of the MLO gene family in 11 Lamiaceae species, providing a manual curated catalog of 324 MLO proteins. Evolutionary history and phylogenetic relationships were studied through maximum likelihood analysis and motif patter reconstruction. Our approach highlighted seven different clades diversified starting from an ancestral MLO domain pattern organized in 18 highly conserved motifs. In addition, 74 Lamiaceae putative PM susceptibility genes, clustering in clade V, were identified. Finally, we performed a codon-based evolutionary analysis, revealing a general high level of purifying selection in the eleven Lamiaceae MLO gene families, and the occurrence of few regions under diversifying selection in candidate susceptibility factors. The results of this work may help to address further biological questions concerning MLOs involved in PM susceptibility. In follow-up studies, it could be investigated whether the silencing or loss-of-function mutations in one or more of these candidate genes may lead to PM resistance.

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events

Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.

Conserved chloroplast genome sequences of the genus Clerodendrum Linn. (Lamiaceae) as a super-barcode

BACKGROUND

The plants of the genus Clerodendrum L. have great potential for development as an ornamental and important herbal resource. There is no significant morphological difference among many species of the genus Clerodendrum, which will lead to confusion among the herbs of this genus and ultimately affect the quality of the herbs. The chloroplast genome will contribute to the development of new markers used for the identification and classification of species.

METHODS AND RESULTS

Here, we obtained the complete chloroplast genome sequences of Clerodendrum chinense (Osbeck) Mabberley and Clerodendrum thomsoniae Balf.f. using the next generation DNA sequencing technology. The chloroplast genomes of the two species all encode a total of 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. A total of 44-42 simple sequence repeats, 19-16 tandem repeats and 44-44 scattered repetitive sequences were identified. Phylogenetic analyses showed that the nine Clerodendrum species were classified into two clades and together formed a monophyletic group. Selective pressure analyses of 77 protein-coding genes showed that there was no gene under positive selection in the Clerodendrum branch. Analyses of sequence divergence found two intergenic regions: trnH-GUG-psbA, nhdD-psaC, exhibiting a high degree of variations. Meanwhile, there was no hypervariable region identified in protein coding genes. However, the sequence identities of these two intergenic spacers (IGSs) are greater than 99% among some species, which will result in the two IGSs not being used to distinguish Clerodendrum species. Analysis of the structure at the LSC (Large single copy) /IR (Inverted repeat) and SSC (Small single copy)/IR boundary regions showed dynamic changes. The above results showed that the complete chloroplast genomes can be used as a super-barcode to identify these Clerodendrum species. The study lay the foundation for the understanding of the evolutionary process of the genus Clerodendrum.

Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory

The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.

Molecular and morphological survey of Lamiaceae species in converted landscapes in Sumatra

Molecular biodiversity surveys have been increasingly applied in hyperdiverse tropical regions as an efficient tool for rapid species assessment of partially undiscovered fauna and flora. This is done by overcoming shortfalls in knowledge or availability of reproductive structures during the sampling period, which often represents a bottleneck for accurate specimens' identification. DNA sequencing technology is intensifying species discovery, and in combination with morphological identification, has been filling gaps in taxonomic knowledge and facilitating species inventories of tropical ecosystems. This study aimed to apply morphological taxonomy and DNA barcoding to assess the occurrence of Lamiaceae species in converted land-use systems (old-growth forest, jungle rubber, rubber, and oil palm) in Sumatra, Indonesia. In this species inventory, we detected 89 specimens of Lamiaceae from 18 species distributed in seven subfamilies from the Lamiaceae group. One third of the species identified in this study lacked sequences in the reference database for at least one of the markers used (matK, rbcL, and ITS). The three loci species-tree recovered a total of 12 out of the 18 species as monophyletic lineages and can be employed as a suitable approach for molecular species assignment in Lamiaceae. However, for taxa with a low level of interspecific genetic distance in the barcode regions used in this study, such as Vitex gamosepala Griff. and V. vestita Wall. ex Walp., or Callicarpa pentandra Roxb. and C. candidans (Burm.f.) Hochr., the use of traditional taxonomy remains indispensable. A change in species composition and decline in abundance is associated with an increase in land-use intensification at the family level (i.e., Lamiaceae), and this tendency might be constant across other plant families. For this reason, the maintenance of forest genetic resources needs to be considered for sustainable agricultural production, especially in hyperdiverse tropical regions. Additionally, with this change in species composition, accurate species identification throughout molecular assignments will become more important for conservation planning.

[Cloning of StHD1 and StHD8 from Schizonepeta tenuifolia and function of regulating glandular trichome development]

Hd-Zip, a unique transcription factor in plant kingdom, influences the growth, development, and secondary metabolism of plants. Hd-zip Ⅳ is thought to play an important role in trichome development of Schizonepeta tenuifolia. This study aims to explore the functions of StHD1 and StHD8 in Hd-zip Ⅳ subfamily in peltate glandular trichome development. To be specific, the expression patterns of the two genes and interaction between the proteins encoded by them were analyzed based on transcriptome sequencing and two-hybrid screening. The subcellular localization was performed and functions of the genes were verified in tobacco and S. tenuifolia. The results showed that StHD1 and StHD8 had high similarity to HD-Zip Ⅳ proteins of other plants and they all had the characteristic conserved domains of HD-Zip Ⅳ subfamily. They were located in the nucleus. The two genes mainly expressed in young tissues and spikes, and StHD1 and StHD8 proteins interacted with each other. The density and length of glandular trichomes increased significantly in tobacco plants with the overexpression of StHD1 and StHD8. Inhibiting the expression of StHD1 and StHD8 by VIGS(virus-induced gene silencing) in S. tenuifolia resulted in the reduction in the density of peltate glandular trichomes, the expression of key genes related to mono-terpene synthesis, and the relative content of limonene and pulegone, the main components of monoterpene. These results suggested that StHD1 and StHD8 of S. tenuifolia formed a complex to regulate glandular trichomes and affect the biosynthesis of monoterpenes.

Mining, expression, and phylogenetic analysis of volatile terpenoid biosynthesis-related genes in different tissues of ten Elsholtzia species based on transcriptomic analysis

We sequenced the leaf and inflorescence transcriptomes of 10 Elsholtzia species to mine genes related to the volatile terpenoid metabolic pathway. A total of 184.68 GB data and 1,231,162,678 clean reads were obtained from 20 Elsholtzia samples, and 333,848 unigenes with an average length of at least 1440 bp were obtained by Trinity assembly. KEGG pathway analysis showed that there were three pathways related to volatile terpene metabolism: terpenoid backbone biosynthesis (No. ko00900), monoterpenoid biosynthesis (No. ko00902), and sesquiterpenoid and triterpenoid biosynthesis (No. ko00909), with 437, 125, and 121 related unigenes, respectively. The essential oil content and composition in 20 Elsholtzia samples were determined by gas chromatography-mass spectrometry. The results showed that there were obvious interspecific differences among the 10 Elsholtzia species, but there were no significant differences between the different tissues among species. The expression levels of seven candidate genes involved in volatile terpenoid biosynthesis in Elsholtzia were further analyzed by quantitative real-time PCR. The results showed that HMGS had the highest expression among all genes, followed by GGPS4. In addition, there was not a significant correlation between the seven genes and the components with high essential oil contents. Combined with the essential oil components detected in this study, the possible biosynthetic pathway of the characteristic components in Elsholtzia plants was speculated to be a metabolic pathway with geraniol as the starting point and elsholtzione as the end product. Phylogenetic analysis was conducted using the nucleotide sequences of the geranyl diphosphate synthase candidate genes, and the results showed that genes related to the volatile terpenoid biosynthetic pathway may be more suitable gene fragments for resolving the Elsholtzia phylogeny.

Sequence Analysis of the Complete Mitochondrial Genome of a Medicinal Plant, Vitex rotundifolia Linnaeus f. (Lamiales: Lamiaceae)

In the present study, we depicted the complete mitochondrial genome of a valuable medicinal plant, Vitex rotundifolia. The mitochondrial genome of V. rotundifolia, mapped as a circular molecule, spanned 380,980 bp in length and had a GC content of 45.54%. The complete genome contained 38 protein-coding genes, 19 transfer RNAs (tRNAs), and 3 ribosomal RNAs (rRNAs). We found that there were only 38.73% (147.54 kb), 36.28% (138.23 kb), and 52.22% (198.96 kb) of the homologous sequences in the mitochondrial genome of V. rotundifolia, as compared with the mitochondrial genomes of Scutellaria tsinyunensis, Boea hygrometrica, and Erythranthe lutea, respectively. A multipartite structure mediated by the homologous recombinations of the three direct repeats was found in the V. rotundifolia mitochondrial genome. The phylogenetic tree was built based on 10 species of Lamiales, using the maximum likelihood method. Moreover, this phylogenetic analysis is the first to present the evolutionary relationship of V. rotundifolia with the other species in Lamiales, based on the complete mitochondrial genome.

Antibacterial Activity and Epigenetic Remodeling of Essential Oils from Calabrian Aromatic Plants

Natural compounds have historically had a wide application in nutrition. Recently, a fundamental role has been identified for essential oils extracted from aromatic plants for their nutritional, antimicrobial, and antioxidant properties, and as food preservatives. In the present study, essential oils (EOs) from ten aromatic plants grown in Calabria (Italy), used routinely to impart aroma and taste to food, were evaluated for their antibacterial activity. This activity was investigated against Escherichia coli strain JM109, and its derived antibiotic-resistant cells selected by growing the strain at low concentrations of ampicillin, ciprofloxacin, and gentamicin by measuring the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC). Although all the essential oils showed bactericidal activity, those from Clinopodium nepeta, Origanum vulgare, and Foeniculum vulgare displayed the greatest inhibitory effects on the bacterial growth of all cell lines. It is plausible that the antibacterial activity is mediated by epigenetic modifications since the tested essential oils induce methylation both at adenine and cytosine residues in the genomes of most cell lines. This study contributes to a further characterization of the properties of essential oils by shedding new light on the molecular mechanisms that mediate these properties.

Integrating RNA-seq with functional expression to analyze the regulation and characterization of genes involved in monoterpenoid biosynthesis in Nepeta tenuifolia Briq

Nepeta tenuifolia Briq. (Lamiaceae) is a medicinal plant historically used in the East Asia region to treat cold and fever, and it is currently used as a clinically effective treatment for respiratory diseases. We previously found that monoterpenoids are the dominant volatile secondary metabolites in N. tenuifolia and their biosynthesis occurs in peltate glandular trichomes. To gain an insight into the molecular mechanisms underlying monoterpenoid biosynthesis in N. tenuifolia, we conducted transcriptome sequencing and examined the expression differences in monoterpene molecular pathway-related genes in different tissues and growth stages by qRT-RCR. In total, six p-menthane monoterpene biosynthetic genes in the (+)-menthone pathway were identified and cloned successfully based on transcriptome data. Moreover, the major constituents, including (+)-limonene, (-)-pulegone and (+)-menthone showed greater accumulation in the spikes than in other organs, such as the expression levels of related key enzyme genes. Additionally, the relative expression of pulegone reductase was the highest at 84 days, showing an inverse trend from (-)-pulegone relative content and leading to (+)-menthone accumulation in peltate glandular trichomes. Finished cloning of the gene for limonene 3-hydroxylase in N. tenuifolia (NtL3OH), heterologous expression in yeast, and in vitro assays were performed for functional characterization. Our study provides an important resource for further research of secondary metabolism of monoterpenes in peltate glandular trichomes of N. tenuifolia and other homologous species.

An extremely promiscuous terpenoid synthase from the Lamiaceae plant Colquhounia coccinea var. mollis catalyzes the formation of sester-/di-/sesqui-/mono-terpenoids

Terpenoids are the largest class of natural products with complex structures and extensive bioactivities; their scaffolds are generated by diverse terpenoid synthases (TPSs) from a limited number of isoprenoid diphosphate precursors. Promiscuous TPSs play important roles in the evolution of terpenoid chemodiversity, but they remain largely unappreciated. Here, an extremely promiscuous terpenoid synthase (CcTPS1) of the TPS-b subfamily was cloned and functionally characterized from a leaf-specific transcriptome of the Lamiaceae plant Colquhounia coccinea var. mollis. CcTPS1 is the first sester-/di-/sesqui-/mono-TPS identified from the plant kingdom, accepting C25/C20/C15/C10 diphosphate substrates to generate a panel of sester-/di-/sesqui-/mono-terpenoids. Engineered Escherichia coli expressing CcTPS1 produced three previously unreported terpenoids (two sesterterpenoids and a diterpenoid) with rare cyclohexane-containing skeletons, along with four sesquiterpenoids and one monoterpenoid. Their structures were elucidated by extensive nuclear magnetic resonance spectroscopy. Nicotiana benthamiana transiently expressing CcTPS1 also produced the diterpenoid and sesquiterpenoids, demonstrating the enzyme's promiscuity in planta. Its highly leaf-specific expression pattern combined with detectable terpenoid products in leaves of C. coccinea var. mollis and N. benthamiana expressing CcTPS1 suggested that CcTPS1 was mainly responsible for diterpenoid and sesquiterpenoid biosynthesis in plants. CcTPS1 expression and the terpenoid products could be induced by methyl jasmonate, suggesting their possible role in plant-environment interaction. CcTPS1 was localized to the cytosol and may differ from mono-TPSs in subcellular compartmentalization and substrate tolerance. These findings will greatly aid our understanding of plant TPS evolution and terpenoid chemodiversity; they also highlight the enormous potential of transcriptome mining and heterologous expression for the exploration of unique enzymes and natural products hidden in plants.

An updated tribal classification of Lamiaceae based on plastome phylogenomics

BACKGROUND

A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data.

RESULTS

We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe.

CONCLUSIONS

Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification.

Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f)

Availability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status of Tectona grandis L.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction/expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested that Tectona could qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as, rps16-trnQ, atpH-atpI, psc4-psbJ, ndhF, rpl32 and ycf1 which have high potential in DNA barcoding applications.

Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants

Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene's lengths of 82,221 bp and 81,450 bp, large single-copy region's (LSC) lengths of 82,221 bp and 81,450 bp, and small single-copy region's (SSC) lengths of 17,363 bp and 17,066 bp, inverted repeat region's (IR) lengths of 51,370 bp and 51,352 bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.

Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

BACKGROUND

Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance.

FINDINGS

We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs.

CONCLUSIONS

Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.

Titanium dioxide nanoparticles (TiO2 NPs) promote growth and ameliorate salinity stress effects on essential oil profile and biochemical attributes of Dracocephalum moldavica

Considering titanium dioxide nanoparticles (TiO2 NPs) role in plant growth and especially in plant tolerance against abiotic stress, a greenhouse experiment was carried out to evaluate TiO2 NPs effects (0, 50, 100 and 200 mg L-1) on agronomic traits of Moldavian balm (Dracocephalum moldavica L.) plants grown under different salinity levels (0, 50 and 100 mM NaCl). Results demonstrated that all agronomic traits were negatively affected under all salinity levels but application of 100 mg L-1 TiO2 NPs mitigated these negative effects. TiO2 NPs application on Moldavian balm grown under salt stress conditions improved all agronomic traits and increased antioxidant enzyme activity compared with plants grown under salinity without TiO2 NP treatment. The application of TiO2 NPs significantly lowered H2O2 concentration. In addition, highest essential oil content (1.19%) was obtained in 100 mg L-1 TiO2 NP-treated plants under control conditions. Comprehensive GC/MS analysis of essential oils showed that geranial, z-citral, geranyl acetate and geraniol were the dominant essential oil components. The highest amounts for geranial, geraniol and z-citral were obtained in 100 mg L-1 TiO2 NP-treated plants under control conditions. In conclusion, application of 100 mg L-1 TiO2 NPs could significantly ameliorate the salinity effects in Moldavian balm.

Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers

The families Lamiaceae and Verbenaceae comprise several closely related species that possess high morphological synapomorphic traits. Hence, there is a tendency of species misidentification using only the morphological characters. Herein, we evaluated the discriminatory power of the universal DNA barcodes (matK and rbcL) for 53 species spanning the two families. Using these markers, we inferred phylogenetic relationships and conducted species delimitation analysis using four delimitation methods: Automated Barcode Gap Discovery (ABGD), TaxonDNA, Bayesian Poisson Tree Processes (bPTP) and General Mixed Yule Coalescent (GMYC). The phylogenetic reconstruction based on the matK gene resolved the relationships between the families and further suggested the expansion of the Lamiaceae to include some core Verbanaceae genus, e.g., Gmelina. The rbcL marker using the TaxonDNA method displayed high species delimitation resolutions, while the ABGD, GMYC, and bPTP generated different number of Operational Taxonomic Units/genetic clusters. Our results underscored the efficiency of the matK and rbcL genes as reliable markers for resolving phylogenetic relationships and species delimitation of both families, respectively. The current study provides insights into the DNA barcode applications in these families, at the same time contributing to the current understanding of genetic divergence patterns in angiosperms.

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.

The effect of purine-type cytokinin on the proliferation and production of phenolic compounds in transformed shoots of Dracocephalum forrestii

Dracocephalum forrestii is a perennial, endemic to China plant with a number of pharmaceutical properties. Transformed shoots of the species spontaneously regenerated from hairy roots induced by Agrobacterium rhizogenes. The transgenic nature of the shoots was confirmed by polymerase chain reaction (PCR). The shoot culture was multiplied on Murashige and Skoog (MS) medium with 0.2 mg/l IAA and 0.2, 0.5, 1.0, 2.0 or 5.0 mg/l purine-type cytokinins (mT, BAR, BPA or BAP). The highest multiplication rate (about thirteen shoot or buds per explant) was obtained on MS medium with 0.2 mg/l mT after four weeks of culture. The phenolic compounds present in the hydromethanolic extracts from the D. forrestii transgenic shoots were characterized using UPLC-PDA-ESI-MS. The shoots were found to biosynthesize three phenolic acids and five flavonoid glycosides. UHPLC analysis of the hydromethanolic extracts found the predominant phenolic acid to be rosmarinic acid, with its highest content observed in shoots cultivated with 5.0 mg/l BPA. In contrast, the greatest production of flavonoid derivatives (especially acacetin derivatives) was observed in the medium supplemented with 2 mg/l BPA.

Iron oxide nanoparticles: a novel elicitor to enhance anticancer flavonoid production and gene expression in Dracocephalum kotschyi hairy-root cultures

BACKGROUND

Dracocephalum kotschyi Boiss. is a valuable source of rosmarinic acid (RA) and methoxylated hydroxyflavones (such as xanthomicrol and cirsimaritin) with antioxidative and antiplatelet effects and with antiproliferative potential against various cancer cells. The extensive application of nanotechnology in hairy root cultures is a new sustainable production platform for producing these active constituents. In the present study, hairy roots derived from 4-week-old leaves and Agrobacterium rhizogenes strain ATCC15834 were used to investigate the impact of various concentrations of iron oxide nanoparticles (Fe NPs) in two elicitation time exposures (24 and 48 h) on growth, antioxidant enzyme activity, total phenolic and flavonoid content (TPC and TFC), and some polyphenols. Gene expression levels of phenylalanine ammonia-lyase (pal) and rosmarinic acid synthase (ras) were also analyzed.

RESULTS

Iron nanoparticles enhanced biomass accumulation in hairy roots. The treatment time and Fe NP dosage largely improved the activity of antioxidant enzymes, TPC and TFC. The highest RA (1194 μg g^-1 FW) content (9.7-fold), compared to controls, was detected with 24 h of exposure to 75 mg L^-1 Fe NP, which was consistent with the expression of pal and ras genes under the influence of elicitation. The xanthomicrol, cirsimaritin, and isokaempferide content was increased 11.87, 3.85, and 2.27-fold, respectively.

CONCLUSION

Stimulation of D. kotschyi hairy roots by Fe NPs led to a significant increase in the induction and production of important pharmaceutical compounds such as rosmarinic acid and xanthomicrol. © 2019 Society of Chemical Industry.

Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants

As a means to maintain their sessile lifestyle amid challenging environments, plants produce an enormous diversity of compounds as chemical defenses against biotic and abiotic insults. The underpinning metabolic pathways that support the biosynthesis of these specialized chemicals in divergent plant species provide a rich arena for understanding the molecular evolution of complex metabolic traits. Rosmarinic acid (RA) is a phenolic natural product first discovered in plants of the mint family (Lamiaceae) and is recognized for its wide range of medicinal properties and potential applications in human dietary and medical interventions. Interestingly, the RA chemotype is present sporadically in multiple taxa of flowering plants as well as some hornworts and ferns, prompting the question whether its biosynthesis arose independently across different lineages. Here we report the elucidation of the RA biosynthetic pathway in Phacelia campanularia (desert bells). This species represents the borage family (Boraginaceae), an RA-producing family closely related to the Lamiaceae within the Lamiids clade. Using a multi-omics approach in combination with functional characterization of candidate genes both in vitro and in vivo, we found that RA biosynthesis in P. campanularia involves specific activities of a BAHD acyltransferase and two cytochrome P450 hydroxylases. Further phylogenetic and comparative structure-function analyses of the P. campanularia RA biosynthetic enzymes clearly indicate that RA biosynthesis has evolved independently at least twice in the Lamiids, an exemplary case of chemotypic convergence through disparate evolutionary trajectories.

Improving the production of podophyllotoxin in hairy roots of Hyptis suaveolens induced from regenerated plantlets

Ten Hyptis suaveolens hairy root lines were established by infecting nodal explants with K599+pGus-GFP+ and ATCC15834+pTDT strains from Agrobacterium rhizogenes. Genetic transformation was confirmed by epifluorescence and plagiotropic hairy root growth in absence of growth regulators. Cytotoxicity was determined using the sulforhodamine B method, and the production of podophyllotoxin (PTOX) was measured by high performance thin layer chromatography scanning. Through these methodologies, HsTD10 was identified as the hairy root line with the highest cytotoxicity and PTOX production, which was corroborated by liquid chromatography-mass spectrometry and micrOTOF-Q II. A suspension culture of HsTD10 was established in which PTOX and carbohydrate consumption during growth kinetics were quantified by high-performance liquid chromatography. Procedures to increase the production and retrieval of PTOX in the HsTD10 line included selection of culture medium, addition of thiamine, and modification of the PTOX extraction method. The best combination of these variables was MS medium at 75% of its components with the addition of 2 mg L^-1 of thiamine, extraction with methanol-dichloromethane, and sonication at 40 ± 5°C. During kinetics, growth-associated PTOX accumulation was observed. The specific growth rate (μ) was 0.11 d^-1. The highest concentration of PTOX obtained with HsTD10 (5.6 mg g^-1 DW) was 100 times higher than that reported for roots of wild plants and 56 times higher than that for in vitro nontransformed roots of H. suaveolens.

Physiological and molecular responses to drought stress in teak (Tectona grandis L.f.)

Drought stress is an increasingly common and worrying phenomenon because it causes a loss of production in both agriculture and forestry. Teak is a tropical tree which needs alternating rainy and dry seasons to produce high-quality wood. However, a robust understanding about the physiological characteristics and genes related to drought stress in this species is lacking. Consequently, after applying moderate and severe drought stress to teak seedlings, an infrared gas analyzer (IRGA) was used to measure different parameters in the leaves. Additionally, using the root transcriptome allowed finding and analyzing the expression of several drought-related genes. As a result, in both water deficit treatments a reduction in photosynthesis, transpiration, stomatal conductance and leaf relative water content was found. As well, an increase in free proline levels and intrinsic water use efficiency was found when compared to the control treatment. Furthermore, 977 transcripts from the root contigs showed functional annotation related to drought stress, and of these, TgTPS1, TgDREB1, TgAREB1 and TgPIP1 were selected. The expression analysis of those genes along with TgHSP1, TgHSP2, TgHSP3 and TgBI (other stress-related genes) showed that with moderate treatment, TgTPS1, TgDREB1, TgAREB1, TgPIP1, TgHSP3 and TgBI genes had higher expression than the control treatment, but with severe treatment only TgTPS1 and TgDREB1 showed higher expression than the control treatment. At the end, a schematic model for the physiological and molecular strategies under drought stress in teak from this study is provided. In conclusion, these physiological and biochemical adjustments in leaves and genetic changes in roots under severe and prolonged water shortage situations can be a limiting factor for teak plantlets' growth. Further studies of those genes under different biotic and abiotic stress treatments are needed.

Characterization of a sesquiterpene cyclase from the glandular trichomes of Leucosceptrum canum for sole production of cedrol in Escherichia coli and Nicotiana benthamiana

Cedrol is an extremely versatile sesquiterpene alcohol that was approved by the Food and Drug Administration of the United States as a flavoring agent or adjuvant and has been commonly used as a flavoring ingredient in cosmetics, foods and medicine. Furthermore, cedrol possesses a wide range of pharmacological properties including sedative, anti-inflammatory and cytotoxic activities. Commercial production of cedrol relies on fractional distillation of cedar wood oils, followed by recrystallization, and little has been reported about its biosynthesis and aspects of synthetic biology. Here, we report the cloning and functional characterization of a cedrol synthase gene (Lc-CedS) from the transcriptome of the glandular trichomes of a woody Lamiaceae plant Leucosceptrum canum. The recombinant Lc-CedS protein catalyzed the in vitro conversion of farnesyl diphosphate into the single product cedrol, suggesting that Lc-CedS is a high-fidelity terpene synthase. Co-expression of Lc-CedS, a farnesyl diphosphate synthase gene and seven genes of the mevalonate (MVA) pathway responsible for converting acetyl-CoA into farnesyl diphosphate in Escherichia coli afforded 363 μg/L cedrol as the sole product under shaking flask conditions. Transient expression of Lc-CedS in Nicotiana benthamiana also resulted in a single product cedrol with a production level of 3.6 μg/g fresh weight. The sole production of cedrol by introducing of Lc-CedS in engineered E. coli and N. benthamiana suggests now alternative production systems using synthetic biology approaches that would better address sufficient supply of cedrol.

Asymmetrical selection maintains heritable phenotypic variation between two subspecies of Monardella villosa

PREMISE

Monardella villosa is an evolutionarily young species complex distributed across a large geographic range. Our goal was to determine whether the phenotypic difference between two subspecies of M. villosa was heritable and whether the alternative phenotypes were adaptive to their respective local habitats.

METHODS

We collected seeds from 25 populations of M. villosa, 14 from subspecies franciscana, which grows closer to the coast, and 11 from subspecies villosa, which has a larger and more inland geographic distribution. We reciprocally transplanted the two subspecies into their respective habitats and compared plant germination, post-emergence survival, and growth. We used linear mixed models to quantify the effects of genotype and environment to determine whether subspecies were locally adapted and whether leaf traits that distinguish these subspecies were genetically based.

RESULTS

Plants of both subspecies grown at the coastal site had significantly lower survival and biomass than the inland site. The subspecies were not locally adapted; however, the coastal subspecies franciscana did have a home site advantage. We also found that distinctive leaf morphological traits were genetically based, with high broad-sense heritability of traits.

CONCLUSIONS

The two subspecies of Monardella villosa were not locally adapted to their respective habitat, but rather we found that selection for local genotypes may be stronger at the coastal site. Despite the lack of evidence for local adaptation in the strict sense, the subspecies had heritable variation in several leaf phenotypes, indicating that heterogeneous selection imposes an adaptive trade-off for leaf trichome production within this species.

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence-secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.

A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae)

Members of the mint family (Lamiaceae) accumulate a wide variety of industrially and medicinally relevant diterpenes. We recently sequenced leaf transcriptomes from 48 phylogenetically diverse Lamiaceae species. Here, we summarize the available chemotaxonomic and enzyme activity data for diterpene synthases (diTPSs) in the Lamiaceae and leverage the new transcriptomes to explore the diTPS sequence and functional space. Candidate genes were selected with an intent to evenly sample the sequence homology space and to focus on species in which diTPS transcripts were found, yet from which no diterpene structures have been previously reported. We functionally characterized nine class II diTPSs and 10 class I diTPSs from 11 distinct plant species and found five class II activities, including two novel activities, as well as a spectrum of class I activities. Among the class II diTPSs, we identified a neo-cleroda-4(18),13E-dienyl diphosphate synthase from Ajuga reptans, catalyzing the likely first step in the biosynthesis of a variety of insect-antifeedant compounds. Among the class I diTPSs was a palustradiene synthase from Origanum majorana, leading to the discovery of specialized diterpenes in that species. Our results provide insights into the diversification of diterpene biosynthesis in the mint family and establish a comprehensive foundation for continued investigation of diterpene biosynthesis in the Lamiaceae.

Lamiophlomis rotata Identification via ITS2 Barcode and Quality Evaluation by UPLC-QTOF-MS Couple with Multivariate Analyses

Lamiophlomis rotata (L. rotata), is known as "Daba" in the Tibetan region, Ajuga ovalifolia and Oreosolen wartii have also been utilized as substitutes for "Daba", however, only L. rotata has been officially listed in the Chinese Pharmacopoeia for hemostasis preparations. To safely apply the traditional uses of the herb, internal transcribed spacer 2 (ITS2) DNA barcodes were employed to discriminate L. rotata from its adulterants. For further evaluation of the quality of different originating habitats, the chemical profiles of 25 samples were determined by ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry (UPLC-QTOF-MS) coupled with multivariate analyses. ITS2 DNA barcodes differentiated L. rotata from O. wartii and A. ovalifolia accurately. A neighbor-joining (NJ) tree showed that three origins clustered into three clades. Forty-nine compounds were identified in the total ion current (TIC) profile of L. rotata. Additionally, two pairs of isomers were identified for the first time by using mass spectrometry fragmentation. The differences between the variable habitats were determined by multivariate statistical analysis of the UPLC-QTOF-MS data from 25 specimens. Ten compounds were identified as the characteristic markers distinguishing the sample from four geographical origins. The results also suggest that samples from Qinghai and Sichuan province would be the most suitable choice for traditional prescriptions and preparations.

Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia

Although several resurrection plant genomes have been sequenced, the lack of suitable dehydration-sensitive outgroups has limited genomic insights into the origin of desiccation tolerance. Here, we utilized a comparative system of closely related desiccation-tolerant (Lindernia brevidens) and -sensitive (Lindernia subracemosa) species to identify gene- and pathway-level changes associated with the evolution of desiccation tolerance. The two high-quality Lindernia genomes we assembled are largely collinear, and over 90% of genes are conserved. L. brevidens and L. subracemosa have evidence of an ancient, shared whole-genome duplication event, and retained genes have neofunctionalized, with desiccation-specific expression in L. brevidens Tandem gene duplicates also are enriched in desiccation-associated functions, including a dramatic expansion of early light-induced proteins from 4 to 26 copies in L. brevidens A comparative differential gene coexpression analysis between L. brevidens and L. subracemosa supports extensive network rewiring across early dehydration, desiccation, and rehydration time courses. Many LATE EMBRYOGENESIS ABUNDANT genes show significantly higher expression in L. brevidens compared with their orthologs in L. subracemosa Coexpression modules uniquely upregulated during desiccation in L. brevidens are enriched with seed-specific and abscisic acid-associated cis-regulatory elements. These modules contain a wide array of seed-associated genes that have no expression in the desiccation-sensitive L. subracemosa Together, these findings suggest that desiccation tolerance evolved through a combination of gene duplications and network-level rewiring of existing seed desiccation pathways.

Amphitropical disjunctions in New World Menthinae: Three Pliocene dispersals to South America following late Miocene dispersal to North America from the Old World

PREMISE OF THE STUDY

The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae.

METHODS

Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS.

KEY RESULTS

A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr.

CONCLUSIONS

Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.

Fatty acid profiling and multivariate analysis in the genus Leucas reveals its nutritional, pharmaceutical and chemotaxonomic significance

Genus Leucas with about 41 species found in India, is an Asian genus with separation from its close relatives in Africa based on phylogenetic evidence. Present study represents the only comprehensive phytochemical investigation on this genus. We have analyzed the seed fatty acid compositions of 26 species and five varieties of Leucas for nutritional, pharmaceutical and chemotaxonomic perspectives. The fatty acids and their composition in seeds of Leucas species, collected from different geographical regions in India, were analyzed by gas chromatography and mass spectrometry. Significant variations have been observed in fatty acid profiles among species and their varieties. We observed major fatty acids as palmitic, stearic, oleic, linoleic and laballenic acid; whereas myristic, palmitoleic, cis-vaccenic, linolenic, eicosanoic, eicosenoic, phlomic and docosanoic acid were detected in minor quantities. Laballenic and phlomic acids are unusual allenic fatty acids found in few Lamiaceae members from order Lamiales. Laballenic acid, a proven molecule of pharmaceutical importance, was observed in all the Leucas species studied. Three species of Leucas; L. helianthimifolia, L. ciliata var. vestita and L. hirta were found to contain ≥40% laballenic acid and can act as potential source for isolation of pharmaceutical compounds. This study also reports the presence of another allenic fatty acid, phlomic acid, in several Leucas species. Principal component analysis and hierarchical cluster analysis showed a distinct separation among the species based on abundance of similar fatty acids. The fatty acid profile appears to be overlapping at higher level and does not support separation of Asian Leucas from its African relatives and the inclusion of Asian taxa in morphologic sections. However, hierarchical clustering of L. helianthimifolia, L. ciliata var. vestita and L. hirta supported treatment under the morphologic section Astrodon. Multivariate analysis on the chemometric data also supported this cluster as the most prominent source of medicinally useful laballenic acid. Based on the FAs profile, a reconsideration of species boundaries in L. ciliata and L. marrubioides species complex is proposed.

Insight into Central Asian flora from the Cenozoic Tianshan montane origin and radiation of Lagochilus (Lamiaceae)

The Tianshan Mountains play a significant role in the Central Asian flora and vegetation. Lagochilus has a distribution concentration in Tianshan Mountains and Central Asia. To investigate generic spatiotemporal evolution, we sampled most Lagochilus species and sequenced six cpDNA locations (rps16, psbA-trnH, matK, trnL-trnF, psbB-psbH, psbK-psbI). We employed BEAST Bayesian inference for dating, and S-DIVA, DEC, and BBM for ancestral area/biome reconstruction. Our results clearly show that the Tianshan Mountains, especially the western Ili-Kirghizia Tianshan, as well as Sunggar and Kaschgar, was the ancestral area. Ancestral biome was mainly in the montane steppe zone of valley and slope at altitudes of 1700–2700 m, and the montane desert zone of foothill and front-hill at 1000–1700 m. Here two sections Inermes and Lagochilus of the genus displayed “uphill” and “downhill” speciation process during middle and later Miocene. The origin and diversification of the genus were explained as coupled with the rapid uplift of the Tianshan Mountains starting in late Oligocene and early Miocene ca. 23.66~19.33 Ma, as well as with uplift of the Qinghai-Tibetan Plateau (QTP) and Central Asian aridification.

The CYCLOIDEA-RADIALIS module regulates petal shape and pigmentation, leading to bilateral corolla symmetry in Torenia fournieri (Linderniaceae)

The diverse pigmentation patterns of flower corollas probably result from pollinator-mediated selection. Previous studies demonstrated that R2R3-MYB factors may have been recruited in the regulation of corolla pigmentation. However, how R2R3-MYBs became so diverse in their regulation of different pigmentation patterns remains unclear. Here, we studied a Lamiales species, Torenia fournieri, which has elaborate zygomorphic flowers with dorsal-ventral asymmetries in corolla pigmentation. We found recent gene duplication events in CYCLOIDEA-like (CYC-like) and RADIALIS-like (RAD-like) genes, and functionally analyzed three dorsal-specific expression factors: TfCYC1, TfCYC2, and TfRAD1. We found that the CYC-RAD module coordinates petal shape and corolla pigmentation, as ectopic expression of TfCYC2 or TfRAD1 disrupted the asymmetric corolla pigmentation pattern and produced strongly dorsalized flowers. Dorsal petal identity was lost when TfCYC2 was down-regulated or when TfRAD1 was knocked out. In T. fournieri, the diversified CYC and RAD genes have evolved regulatory loops, and TfCYC2 binds directly to the regulatory regions of an R2R3-MYB factor gene, TfMYB1, which might lead to its asymmetric expression and ultimately establish the asymmetric pigmentation pattern. These findings support the existence of a regulatory module that integrates dorsal-ventral patterning and asymmetric corolla pigmentation in T. fournieri.

Dissecting the proteome dynamics of the salt stress induced changes in the leaf of diploid and autotetraploid Paulownia fortunei

Exposure to high salinity can trigger acclimation in many plants. Such an adaptative response is greatly advantageous for plants and involves extensive reprogramming at the molecular level. Acclimation allows plants to survive in environments that are prone to increasing salinity. In this study, diploid and autotetraploid Paulownia fortunei seedlings were used to detect alterations in leaf proteins in plants under salt stress. Up to 152 differentially abundant proteins were identified by Multiplex run iTRAQ-based quantitative proteomic and LC-MS/MS methods. Bioinformatics analysis suggested that P. fortunei leaves reacted to salt stress through a combination of common responses, such as induced metabolism, signal transduction, and regulation of transcription. This study offers a better understanding of the mechanisms of salt tolerance in P. fortunei and provides a list of potential target genes that could be engineered for salt acclimation in plants, especially trees.

Repeated and diverse losses of corolla bilateral symmetry in the Lamiaceae

BACKGROUND AND AIMS

Independent evolution of derived complex characters provides a unique opportunity to assess whether and how similar genetic changes correlate with morphological convergence. Bilaterally symmetrical corollas have evolved multiple times independently from radially symmetrical ancestors and likely represent adaptations to attract specific pollinators. On the other hand, losses of bilateral corolla symmetry have occurred sporadically in various groups, due to either modification of bilaterally symmetrical corollas in late development or early establishment of radial symmetry.

METHODS

This study integrated phylogenetic, scanning electron microscopy (SEM)-based morphological, and gene expression approaches to assess the possible mechanisms underlying independent evolutionary losses of corolla bilateral symmetry.

KEY RESULTS

This work compared three species of Lamiaceae having radially symmetrical mature corollas with a representative sister taxon having bilaterally symmetrical corollas and found that each reaches radial symmetry in a different way. Higher core Lamiales share a common duplication in the CYCLOIDEA (CYC ) 2 gene lineage and show conserved and asymmetrical expression of CYC2 clade and RAD genes along the adaxial-abaxial floral axis in species having bilateral corolla symmetry. In Lycopus americanus , the development and expression pattern of La-CYC2A and La-CYC2B are similar to those of their bilaterally symmetrical relatives, whereas the loss of La-RAD expression correlates with a late switch to radial corolla symmetry. In Mentha longifolia , late radial symmetry may be explained by the loss of Ml-CYC2A , and by altered expression of two Ml-CYC2B and Ml-RAD genes . Finally, expanded expression of Cc-CYC2A and Cc-RAD strongly correlates with the early development of radially symmetrical corollas in Callicarpa cathayana .

CONCLUSIONS

Repeated losses of mature corolla bilateral symmetry in Lamiaceae are not uncommon, and may be achieved by distinct mechanisms and various changes to symmetry genes, including the loss of a CYC2 clade gene from the genome, and/or contraction, expansion or alteration of CYC2 clade and RAD -like gene expression.

Transcriptomic analyses reveal biosynthetic genes related to rosmarinic acid in Dracocephalum tanguticum

Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which 'biosynthesis of secondary metabolites' is the second enriched pathway. Furthermore, rosmarinic acid (RA) is one of the multifunctional phenolic bioactive compounds produced in some Lamiaceae species. The six organs of D. tanguticum were confirmed to produce RA. A total of 22 predicted biosynthetic genes related to RA from the transcriptome were further isolated. Two of these genes were identified as candidates by evaluating the correlation coefficient between the RA contents and the expression of the predicted biosynthetic genes in the six organs. The new sequence information will improve the knowledge of D. tanguticum, as well as provide a reference tool for future studies of biosynthetic genes related to RA in this species.

New chromosome reports in Lamiaceae of Kashmir (Northwest Himalaya), India

Meiotic studies and chromosome data are imperative in order to have an overall germplasm evaluation of a taxon. In the present effort, the meiotic study is carried out in 48 populations belonging to 26 species of Lamiaceae collected from their natural habitats in Kashmir Himalaya, which forms an important part of Northwest Himalaya. Chromosome counts in the five species viz. Dracocephalum nutans (2n = 10), Lycopus europaeus (2n = 22), Marrubium vulgare (2n = 54), Nepeta nervosa (2n = 18) and Salvia sclarea (2n = 22) are first time reported from India. Besides, 17 species are cytologically evaluated for the first time from the study area-Kashmir Himalaya. In Marrubium vulgare, hexaploid cytotype (2n = 6 × =54) is reported for the first time. Also, diploid and tetraploid cytomorphovariants are observed in Calamintha vulgaris (2n = 20, 40), Elsholtzia ciliata (2n = 16, 32) and Mentha longifolia (2n = 20, 40). Various meiotic abnormalities like chromatin stickiness, cytomixis, nonsynchronous disjunction, laggards, chromatin bridges, etc. leading to pollen abnormalities have been documented for the first time in some species. The worldwide status of chromosome number data in each genus is presented.

Effect of discrete (individual) and mixed (bulk) genomic DNA on genetic diversity estimates and population structure in Teak (Tectona grandis L. f.)

Teak (Tectona grandis L.f.), a paragon timber tree of tropical deciduous forests of Central and Peninsular India, is highly prized for its wood colour, decorative grains, durability and lightness. An experiment was carried out to compare the genetic variation detected and genetic relationships inferred in five teak populations via 10 genomic DNA samples per population each of either single seed or bulk of 3- or 5- seeds with the help of ISSR markers. The genomic DNA of single seed exhibited higher number of polymorphic loci, per cent polymorphism, nei’s genetic diversity and shannon Information Index than the bulk genomic DNA of 3- or 5- seeds. The bulking of genomic DNA of 3- and 5- seeds using Nei’s genetic distance coefficient revealed similar genetic relationships, which were at variance with those in single seed treatment. Mantel’s correlation test among the genetic distance matrices of single seed sampling, 3-seed bulk and 5-seed bulk sampling also confirmed the trend. Since the bulking of genomic DNA did not generate compatible estimates of diversity parameters and genetic relationship of five populations from its single seed sampling, we recommend strict guarding of identities of genotypes within the collected samples for obtaining precise estimates and drawing accurate conclusions about the genetic diversity and clustering of populations.

Selective in vitro and in silico butyrylcholinesterase inhibitory activity of diterpenes and rosmarinic acid isolated from Perovskia atriplicifolia Benth. and Salvia glutinosa L

Cholinesterase inhibition is one of the most treatment strategies against Alzheimer's disease (AD) where metal accumulation is also strongly associated with pathology of the disease. In the current study, we assessed inhibitory effect against acetyl- (AChE) and butyrylcholinesterase (BChE) and metal-chelating capacity of twelve diterpenes: arucadiol, miltirone, tanshinone IIa, 1-oxomiltirone, cryptotanshinone, 1,2-didehydromiltirone, 1,2-didehydrotanshinone IIa, 1β-hydroxycryptotanshinone, 15,16-dihydrotanshinone, tanshinone I, isotanshinone II, 1(S)-hydroxytanshinone IIa, and rosmarinic acid, isolated from Perovskia atriplicifolia and Salvia glutinosa. The compounds were tested at 10 μg/mL using ELISA microtiter assays against AChE and BChE. QSAR and molecular docking studies have been also performed on the active compounds. All of the compounds showed higher [e.g., IC50 = 1.12 ± 0.07 μg/mL for 1,2-didehydromiltirone, IC50 = 1.15 ± 0.07 μg/mL for cryptotanshinone, IC50 = 1.20 ± 0.03 μg/mL for arucadiol, etc.)] or closer [1,2-didehydrotanshinone IIa (IC50 = 5.98 ± 0.49 μg/mL) and 1(S)-hydroxytanshinone IIa (IC50 = 5.71 ± 0.27 μg/mL)] inhibition against BChE as compared to that of galanthamine (IC50 = 12.56 ± 0.37 μg/mL), whereas only 15,16-dihydrotanshinone moderately inhibited AChE (65.17 ± 1.39%). 1,2-Didehydrotanshinone IIa (48.94 ± 0.26%) and 1(S)-hydroxytanshinone IIa (47.18 ± 5.10%) possessed the highest metal-chelation capacity. The present study affords an evidence for the fact that selective BChE inhibitors should be further investigated as promising candidate molecules for AD therapy.

AM fungi patchiness and the clonal growth of Glechoma hederacea in heterogeneous environments

The effect of AM fungi spatial distribution on individual plant development may determine the dynamics of the whole plant community. We investigated whether clonal plants display, like for other resources, a foraging or a specialization response, to adapt to the distribution of AM fungi. Two separate experiments were done to investigate the response of Glechoma hederacea to a heterogeneous distribution of a mixture of 3 AM fungi species, and the effects of each species on colonization and allocation traits. No specialization and a limited foraging response to the heterogeneous distribution of AM fungi was observed. An effect of the AM fungal species on plant mass allocation and ramet production, but not on spacer length, was detected. Two possible explanations are proposed: (i) the plant's responses are buffered by differences in individual effects of the fungal species or their root colonization intensity. (ii) the initial heterogeneous distribution of AM fungi is perceived as homogeneous by the plant either by reduced physiological integration or due to the transfer of AM fungi propagules through the stolons. Microscopic and DNA sequencing analyses provided evidence of this transfer, thus demonstrating the role of stolons as dispersal vectors of AM fungi within the plant clonal network.

rDNA Loci Evolution in the Genus Glechoma (Lamiaceae)

Glechoma L. (Lamiaceae) is distributed in eastern Asia and Europe. Understanding chromosome evolution in Glechoma has been strongly hampered by its small chromosomes, constant karyotype and polyploidy. Here phylogenetic patterns and chromosomal variation in Glechoma species are considered, using genome sizes, chromosome mapping of 5S and 35S rDNAs by fluorescence in situ hybridisation (FISH), and phylogenetic analyses of internal transcribed spacers (nrITS) of 35S rDNA and 5S rDNA NTS sequences. Species and populations of Glechoma are tetraploid (2n = 36) with base chromosome number of x = 9. Four chromosomes carry pericentric 5S rDNA sites in their short arms in all the species. Two to four of these chromosomes also carry 35S rDNA in subterminal regions of the same arms. Two to four other chromosomes have 35S rDNA sites, all located subterminally within short arms; one individual possessed additional weak pericentric 35S rDNA signals on three other chromosomes. Five types of rDNA locus distribution have been defined on the basis of 35S rDNA variation, but none is species-specific, and most species have more than one type. Glechoma hederacea has four types. Genome size in Glechoma ranges from 0.80 to 0.94 pg (1C), with low levels of intrapopulational variation in all species. Phylogenetic analyses of ITS and NTS sequences distinguish three main clades coinciding with geographical distribution: European (G. hederacea–G. hirsuta), Chinese and Korean (G. longituba), and Japanese (G. grandis). The paper presents the first comparative cytogenetic analyses of Glechoma species including karyotype structure, rDNA location and number, and genome size interpreted in a phylogenetic context. The observed variation suggests that the genus is still in genomic flux. Genome size, but not rDNA loci number and distribution, provides a character for species delimitation which allows better inferences of interspecific relationships to be made, in the absence of well-defined morphological differentiation.

[Phenotypic Trait Variation, Correlation and Path Analysis of Clerodendranthus spicatus]

OBJECTIVE

To investigate the phenotypic trait variation range of Clerodendranthus spicatus, and to look for phenotypic traits closely related with its yield and quality, in order to provide reference for its breeding.

METHODS

Randomly labelled plants of Clerodendranthus spicatus, observed its phenotypic traits and analyzed by variation, principal component, correlation and path analysis.

RESULTS

13 phenotypic traits in the 15 germplasms of Clerodendranthus spicatus had great variations, the variations mainly distributed in yield, growth and genetic characteristics. Correlation and path analysis showed that, the plant dry weight had an extremely significantly positive correlation with fresh weight, and a positive correlation with stem height, stem diameter and root diameter. Plant fresh weight had a majorly direct contribution to the plant dry weight, stem height, stem diameter and root diameter also had a direct contribution to the plant dry weight. The other characters, including root length, branches, the number of leaf nodes, leaf number, leaf length, leaf width, fresh weight/dry weight ratio, rosmarinic acid content and ursolic acid content all had a negatively direct contribution to the plant dry weight. Rosmarinic acid content had a positive correlation with fresh weight, and a significantly positive correlation with fresh weight/dry weight ratio. Fresh weight had a majorly direct contribution to the rosmarinic acid content, stem height and stem diameter also had a direct contribution to the plant rosmarinic acid content. The other characters, including root length, root diameter, branches, the number of leaf nodes, leaf length, leaf width, dry weight, fresh weight/dry weight ratio, and ursolic acid content all had a negatively direct contribution to the rosmarinic acid content.

CONCLUSION

The phenotypic traits of Clerodendranthus spicatus had rich variations on yield, growth and genetic characteristics. When choosing good germplasm, plant fresh weight, stem height, stem diameter and plant fresh weight/dry weight ratio having promoting effects on the plant dry weight and rosmarinic acid content should be considered comprehensively, and plant with vigorous growth, tall stem and more leaves can be choosed firstly.

Heterologous expression and comparative characterization of vacuolar invertases from Cu-tolerant and non-tolerant populations of Elsholtzia haichowensis

Vacuolar invertases (VINs) from Cu-tolerant and non-tolerant populations of Elsholtzia haichowensis have similar enzyme properties, and the enzyme protein divergences contribute little to the varied VIN activities between the contrasting populations. In our previous studies of Elsholtzia haichowensis, vacuolar invertase (VIN) activity in roots of a Cu-tolerant population was found to be significantly higher than that of a non-tolerant population under Cu stress. Divergences of amino acid residues in a sucrose-binding box and other regions of the VINs were detected. To test whether the amino acid divergences influence the enzyme properties of VINs, and thus are relevant to the differences in enzyme activities between the contrasting populations of E. haichowensis, two VIN genes from the Cu-tolerant population (EhCvINV) and non-tolerant population (EhNvINV) were heterologously expressed in Pichia pastoris, and the enzyme properties of the recombinants were characterized and compared. Both of the recombinant enzymes showed temperature optima of 70 °C and pH optima of 4.5-5.5. Copper as well as other heavy metals caused almost the same inhibition to EhNvINV and EhCvINV. No statistically significant differences were observed between EhNvINV and EhCvINV in K m and k cat values for sucrose. The results provided evidence that the observed residue divergences had little influence on the enzyme properties of VIN in E. haichowensis, and the varied VIN activities between the contrasting populations under Cu stress were not relevant to the amino acid divergences in the proteins. Also, some other possible reasons accounting for this difference in invertase activities were discussed, such as up-regulation of expression of the EhCvINV gene under Cu stress, as Cu tolerance mechanisms in Cu-mine plants.

New insights into evolutionary relationships within the subfamily Lamioideae (Lamiaceae) based on pentatricopeptide repeat (PPR) nuclear DNA sequences

PREMISE OF THE STUDY

Lamioideae, one of the most species-rich subfamilies within Lamiaceae, exhibits a remarkable diversity in morphology and habit and is found in many temperate to subtropical regions across the globe. Previous studies based on chloroplast DNA (cpDNA) sequence data produced a tribal classification of Lamioideae, but so far this has not been confirmed with nuclear DNA loci.

METHODS

We investigated sequence variation in a low-copy nuclear pentatricopeptide repeat (PPR) region and compared the phylogenetic results with previously published sequence data from a concatenated data set comprising four cpDNA loci. We incorporated representatives of all 10 lamioid tribes and some unclassified taxa, analyzed the data using phylogenetic inference, and estimated divergence times and ancestral areas for major nodes.

KEY RESULTS

Our results showed overall topological similarities between the cpDNA and PPR phylogenies with strong support for most tribes. However, we also observed incongruence in the circumscription of some tribes, including Gomphostemmateae and Pogostemoneae and in the relationships among tribes. Our results suggest an Oligocene-Miocene origin of the Lamioideae crown group. Asia and the Mediterranean region appear to have been centers of diversity and place of origin for many lamioid tribes.

CONCLUSIONS

This study represents the first phylogeny of subfamily Lamioideae inferred from low-copy nuclear DNA data. We show that most lamioid tribes are corroborated, although the exact circumscription of two tribes is questioned. We have shed further light on the evolutionary relationships within Lamioideae, and this study demonstrates the utility of the PPR region for such subfamilial-level phylogenetic studies.