Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

Background and Aims Zanthoxylum is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny of Zanthoxylum. In this study, we employed target-enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications of Zanthoxylum were evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events.MethodsA custom bait set targeting 354 genes, with a median of 321 bp, was designed for Zanthoxylum and applied to 44 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and maximum likelihood methods based on concatenated datasets. Concordance was assessed using quartet sampling. Additional phylogenetic analyses were performed on putative single and low-copy genes extracted from off-target reads.Key ResultsFour major clades are supported within Zanthoxylum: the African clade, the Z. asiaticum clade, the Asian–Pacific–Australian clade and the American–eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting in the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections of Zanthoxylum are resolved as monophyletic.ConclusionsTarget enrichment is suitable for assessing phylogenetic relationships in Zanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.     

Distribution of unsaturated aliphatic acid amides in japanese Zanthoxylum species

Seven species and two varieties of Zanthoxylum in Japan were investigated for unsaturated aliphatic acid amides. In addition to the known amides α-sanshoöl, γ-sanshoöl and hydroxy-γ-sanshoöl, a new compound, hydroxy-α-sanshoöl, was isolated and established by chemical and spectroscopic evidence. The compounds, corresponding to hydroxyl derivatives of the amides in the barks, commonly existed in the pericarps of all collected materials. Japanese Zanthoxylum species were divided chemotaxonomically into two taxa. These taxa ditter from the two assigned on the basis of botanical classification.     

Phylogenetic relationships among cultivated <Emphasis Type="Italic">Zanthoxylum</Emphasis> species in China based on cpDNA markers

We here present a molecular phylogenetic analysis of cultivated Zanthoxylum species which have a long history of cultivation both for economic and for chemical values in China. Three cpDNA markers, including matK, rbcL, and trnL-F, were sequenced, with the goals of untangling phylogenetic relationships and inferring biogeographic origin and patterns of distribution among Zanthoxylum species. Based on three cpDNA markers, 19 haplotypes with 64 polymorphic sites in Zanthoxylum provenances were identified in our study. A low genetic differentiation (G _ST ?=?0.271, N _ST ?=?0.373) was observed within Zanthoxylum provenances. Based on phylogenetic tree and haplotype network, all 19 haplotypes were grouped into six clusters. Our results also supported the hypothesis that the so-called “Green Huajiao” belongs to the species Zanthoxylum armatum rather than Zanthoxylum schinifolium. The results also revealed that haplotypes of two cultivated species, Zanthoxylum bungeanum and Z. armatum, most probably diverged during the Late Miocene. Ancestral area reconstruction indicated that cultivated Zanthoxylum species experienced multiple long-distance dispersal events and several vicariance events and the ancestors of Zanthoxylum first colonized Yunnan and Guizhou provinces (D). Accordingly, the current disjunct distribution of Z. bungeanum and Z. armatum may represent long-distance dispersal of ancestors popularly named “Dahongpao” and “Qinghuajiao,” respectively. It is concluded that cpDNA markers may provide a new conceptual and practical opportunity to evaluate genetic diversity and to identify local cultivars of Zanthoxylum, making it a valuable source to include into potential breeding programs.     

Genetic structure of cultivated <Emphasis Type="Italic">Zanthoxylum</Emphasis> species investigated with SSR markers

Zanthoxylum is an economically and ecologically important genus of the Rutaceae family, of which Z. bungeanum and Z. armatum have a long history of cultivation in China. However, how the natural processes such as selection and drift and agriculture practices have influenced the genetic variation of cultivated Zanthoxylum species during long-term domestication remains elusive. Herein, we determined the population genetic structure of current widely cultivated Zanthoxylum species, Z. bungeanum and Z. armatum. Microsatellite markers revealed a high level of genetic variation and significant genetic differentiation for both species despite Z. bungeanum showed higher genetic diversity than Z. armatum. AMOVA indicated that most of the genetic variation exists within individuals rather than among provenances for both species. Population structure analyses generated three distinct groups within the entire accessions. All Z. bungeanum accessions were distinguished into two major geographic groups, north and south groups, with Qinling Mountains as the main geographic barrier to gene flow while a significant genetic differentiation was observed between cultivated and wild Z. armatum accessions. Mantel test of Z. bungeanum displayed a significant correlation between genetic and geographic distances within each inferred group but no correlation between genetic and geographic distance was observed when comparing genetic and geographic distances focusing only on pairwise of north vs. south provenances, ruling out the hypothesis that gene flow between north and south provenances followed an isolation-by-distance model. Our research provided a fundamental genetic profile that will improve the conservation and responsible exploitation of the extant germplasm of Zanthoxylum.     

Chemical constituents from the leaves of Zanthoxylum nitidum (Roxb.) DC

Twelve compounds were isolated from the ethyl acetate soluble portion of the 70% hydroalcoholic extract from the leaves of Zanthoxylum nitidum (Roxb.) DC. All of the compounds were determined on the basis of UV, IR, NMR and MS and comparison with literature. Among them, compounds 4, 7, 10 and 12 were first acquired from Rutaceae, compound 2 was isolated from the genus of Zanthoxylum for the first time and compounds 1, 3, 6, 9, 11 were isolated from Z. nitidum for the first time. Our present study exhibited the taxonomic relationships between Z. nitidum and other species in the same genus; those between Rutaceae and other families. Furthermore, we have summarized the chemotaxonomic significance of these compounds in Rutaceae and Zanthoxylum.     

Alkaloids and other constituents of Zanthoxylum williamsii,Z. monophyllum and Z. fagara

Zanthoxylum williamsii (Rutaceae) was found to contain (+)-asaranin, (+)-sesamin, esculetin dimethyl ether, nitidine, chelerythrine, magnoflorine, laurifoline, skimmianine and edulinine. The quaternary alkaloid fraction of Z. monophyllum contained berberine, magnoflorine, chelerythrine and a 1,2,9,10-substituted dihydroxydimethoxy-N,N-dimethylaporphinium salt. Leaves of Z. fagara were found to contain synephrine. Leaves of each species were examined for the presence of bishordeninyl terpene alkaloids, but none was found. Some chemotaxonomic relationships among Zanthoxylum species are discussed.     

Metabolomics and proteomics profiles of some medicinal plants and correlation with BDNF activity

BackgroundIdentification of the low abundance of phytochemicals in plant extracts is very difficult. Pharmacological activity observed in such plants is not due to a single compound. In most cases, plant extracts show activity based on synergistic or antagonistic effects. Therefore, the idea of a holistic approach is more rational.PurposeThis study was planned to compare the metabolomics and proteomics profiles of Valeriana officinalis L. (Valerianaceae), Melissa officinalis L. (Lamiaceae), Hypericum perforatum L. (Hypericaceae) and Passiflora incarnata L. (Passifloraceae) used in sedative anxiolytic and sleep disorders. Integrated omics analyses were used to provide a better understanding of the effect of plant extracts on the brain-derived neurotrophic factor (BDNF) expression levels on the SH-SY5Y cell line by a holistic approach.MethodsMetabolomic profiling of the plants was performed using the GC–MS and LC-qTOF-MS systems, and the proteomics analysis using the LC-qTOF-MS system after trypsin digestion. The Human BDNF Quantikine ELISA kit was utilized to test BDNF expression activity on the SH-SY5Y cell line.ResultsThe investigated plant extracts showed a significant increase in BDNF expression (p < 0.05). M. officinalis was found as the most active extract. According to the correlation analyses between BDNF activity and metabolomics or proteomics level, 94 metabolites had a positive correlation while 23 metabolites had a highly negative correlation; those for proteins are 24 and 6, respectively.ConclusionThe multivariate data analysis revealed a similar metabolomics profile of H. perforatum and P. incarnata, which also had a similar activity profile. Remarkably, all the primary metabolites belonging to the Krebs Cycle (citric acid, fumaric acid, succinic acid, pyruvic acid, malic acid and citramalic acid, an analog of malic acid) were positively correlated with BDNF activity. Secondary metabolites with a high BDNF expression belonged to flavonoids, xanthone, coumarines, tannin, naphtalenes, terpenoids and carotenoid skeleton. Two proteins from the cytochrome P450 family (P450 71B11 and P450 94B3) were positively correlated with BDNF activity. Employing omics technologies in the plant research area will offer a better understanding of the role of plant extracts and may lead to the discovery of new compounds with specific activity.     

Chemical constituents from the pericarps of Zanthoxylum bungeanum and their chemotaxonomic significance

The phytochemical study of the pericarps of Zanthoxylum bungeanum Maxim under the guidance of bioactivity led to the isolation of 18 compounds, including a new isobutylhydroxyamide (1) and 17 known compounds, i.e. six alkylamides (2–7), five coumarins (8–12), one benzene derivative (13), three flavonoids (14–16), and two sterols (17–18). Their structures were elucidated based on extensive spectroscopic methods (HRESIMS, 1D and 2D NMR experiments) and by comparison with literature data. New compound (1) and known compound (2) are cis-trans isomeric isobutylhydroxyamides. Among them, compounds 9, 10, and 12 were isolated for the first time from Z. bungeanum, compound 11 was firstly recovered from the genus Zanthoxylum, and compound 14 was reported for the first time from the Rutaceae family. The chemotaxonomic significance of isolated compounds from Z. bungeanum is discussed.     

Analysis of diversity amongst widely distributed and endemic Atalantia (family Rutaceae) species from Western Ghats of India

The genus Atalantia Correa is represented in India with four species and two varieties. The infra — generic classification and the species limits in Atalantia are, however, not well defined, due to the occurrence of intermediate forms. Two species, A. racemosa Wight and A. monophylla (L.) DC., are widely distributed, while the third species, A. wightii Tanaka is endemic in the Western Ghats, a well-known biodiversity hotspot. PCR-based methods have been commonly used for the assessment of genetic diversity in plants. We report for the first time the genetic diversity within and between populations of the above three species using two Single Primer Amplification Reaction (SPAR) methods. AMOVA analysis clearly indicates the lesser diversity among the species than within them. The UPGMA tree included all of the doubtful species in one single sub-cluster within the major cluster of A. racemosa and A. wightii, suggesting that these are probably hybrids derived from these two species. At the population level, all A. monophylla populations grouped together in a cluster that was clearly separated from all other species and populations.Key words: AMOVA, Atalantia, diversity, PCA, Rutaceae, SPAR methods, Western Ghats     

The geometric approach to explore the Bactrocera tau complex (Diptera: Tephritidae) in Thailand

Specimens of the genus Bactrocera were collected from several host plants in northern and western Thailand. They were morphologically recognized as Bactrocera tau and were subdivided into eleven samples according to host plant, geographic origin and time of collection. Twelve landmarks of the right wing were described in a total of 264 males and 276 females. An exploratory analysis using kernel density estimates was performed on the multivariate morphometric space. Non-parametric classification highlighted the existence of two non-overlapping clusters within both males and females. The clusters were not congruent with geography. One cluster (cluster I) contained only one plant, Momordica cochinchinensis, the other one (cluster II) contained five different plants including M. cochinchinensis. Further morphometric analyses on selected samples indicated that the influence of the plants on the shape of the wing could not explain satisfactorily the presence of two clusters. Genetic techniques identified the presence of B. tau cryptic species C in M. cochinchinensis from cluster I, and of B. tau cryptic species A in Coccinia grandis from cluster II. Our working hypothesis is that the two clusters identified by geometric morphometrics were species A and C, respectively.     

Foliicole flechten aus zaire (III) Die GattungByssoloma Trevisan

Nine species ofByssoloma Trevisan (Pilocarpaceae) are reported from a collection of foliicolous lichens from Zaire, and includeB. murinum sp. n. In addition,B. usambarense sp. n. is described from adjacent Tanzania. A determination key is provided to all the known African species, and each species is briefly characterized.     

Chemical constituents from the fruits of Zanthoxylum bungeanum and their chemotaxonomic significance

The phytochemical study of the fruits of Zanthoxylum bungeanum Maxim led to the isolation of sixteen compounds, including a new compound zantharin (1) and fifteen other known compounds, which consist of ten coumarins (2–11), three alkaloids (12–14), and two phenols (15–16). Their structures were elucidated based on extensive spectroscopic methods (1D and 2D NMR, HRESIMS, UV, and IR experiments) and by comparison with literature data. In this work, all the compounds were isolated from Z. bungeanum for the first time, in which, compounds 5 and 13–16 were reported for the first time from the genus Zanthoxylum and the Rutaceae family, respectively. Moreover, the chemotaxonomic significance of isolated compounds is discussed.     

The chemotaxonomic classification of Korean Campanulaceae based on triterpene,sterol, and polyacetylene contents

The taxonomic usefulness of selected marker compounds was investigated by analyzing the chemotaxonomy of 25 taxa in the Korean Campanulaceae. Our data permit discrimination of the source plants of crude drugs listed in the Korean Pharmacopoeia and the Korean Herbal Pharmacopoeia. Chemotaxonomic analysis methods were validated, and quantitative measurements of six marker compounds were made using HPLC. Marker compound similarities among taxa were identified through multivariate statistical analyses (principal component analysis and hierarchical cluster analysis). The chemical analysis method was validated with regard to linearity, lower limit of detection, lower limit of quantitation, precision, accuracy, and recovery. The analysis revealed differences in the marker compound composition of each genus. Eight genera comprising Adenophora, Codonopsis, Asyneuma, Campanula, Hanabusaya, Platycodon, Wahlenbergia, and Peracarpa clustered according to the chemical classification. The results indicated that the six marker compounds used in this analysis were useful in identifying Korean Campanulaceae. These marker compound data were able to successfully discriminate among the three species that are sold as the crude drug Adenophorae Radix.     

Metabolic classification of South American Ilex species by NMR-based metabolomics

The genus Ilex to which mate (Ilex paraguariensis) belongs, consists of more than 500 species. A wide range of metabolites including saponins and phenylpropanoids has been reported from Ilex species. However, despite the previous works on the Ilex metabolites, the metabolic similarities between species which can be used for chemotaxonomy of the species are not clear yet. In this study, nuclear magnetic resonance (NMR) spectroscopy-based metabolomics was applied to the classification of 11 South American Ilex species, namely, Ilex argentina, Ilex brasiliensis, Ilex brevicuspis, Ilex dumosa var. dumosa, I. dumosa var. guaranina, Ilex integerrima, Ilex microdonta, I. paraguariensis var. paraguariensis, Ilex pseudobuxus, Ilex taubertiana, and Ilex theezans. ¹H NMR combined with principal component analysis (PCA), partial least square-discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) showed a clear separation between species and resulted in four groups based on metabolomic similarities. The signal congestion of ¹H NMR spectra was overcome by the implementation of two-dimensional (2D)-J-resolved and heteronuclear single quantum coherence (HSQC). From the results obtained by 1D- and 2D-NMR-based metabolomics it was concluded that species included in group A (I. paraguariensis) were metabolically characterized by a higher amount of xanthines, and phenolics including phenylpropanoids and flavonoids; group B (I. dumosa var. dumosa and I. dumosa var. guaranina) with oleanane type saponins; group C (I. brasiliensis, I. integerrima, I. pseudobuxus and I. theezans) with arbutin and dicaffeoylquinic acids, and group D (I. argentina, I. brevicuspis, I. microdonta and I. taubertiana) with the highest level of ursane-type saponins. Clear metabolomic discrimination of Ilex species and varieties in this study makes the chemotaxonomic classification of Ilex species possible.     

Metabolomics as a Potential Chemotaxonomical Tool: Application in the Genus Vernonia Schreb

The taxonomic classification of the genus Vernonia Schreb is complex and, as yet, unclear. We here report the use of untargeted metabolomics approaches, followed by multivariate analyses methods and a phytochemical characterization of ten Vernonia species. Metabolic fingerprints were obtained by accurate mass measurements and used to determine the phytochemical similarities and differences between species through multivariate analyses approaches. Principal component analysis based on the relative levels of 528 metabolites, indicated that the ten species could be clustered into four groups. Thereby, V. polyanthes was the only species with presence of flavones chrysoeriol-7-O-glycuronyl, acacetin-7-O-glycuronyl and sesquiterpenes lactones piptocarphin A and piptocarphin B, while glaucolide A was detected in both V. brasiliana and V. polyanthes, separating these species from the two other species of the Vernonanthura group. Species from the Lessingianthus group were unique in showing a positive response in the foam test, suggesting the presence of saponins, which could be confirmed by metabolite annotation. V. rufogrisea showed a great variety of sesquiterpene lactones, placing this species into a separate group. Species within the Chrysolaena group were unique in accumulating clovamide. Our results of LC-MS-based profiling combined with multivariate analyses suggest that metabolomics approaches, such as untargeted LC-MS, may be potentially used as a large-scale chemotaxonomical tool, in addition to classical morphological and cytotaxonomical approaches, in order to facilitate taxonomical classifications.     

Comparative metabolomics approach coupled with cell- and gene-based assays for species classification and anti-inflammatory bioactivity validation of Echinacea plants

Echinacea preparations were the top-selling herbal supplements or medicines in the past decade; however, there is still frequent misidentification or substitution of the Echinacea plant species in the commercial Echinacea products with not well chemically defined compositions in a specific preparation. In this report, a comparative metabolomics study, integrating supercritical fluid extraction, gas chromatography/mass spectrometry and data mining, demonstrates that the three most used medicinal Echinacea species, Echinacea purpurea, E. pallida, and E. angustifolia, can be easily classified by the distribution and relative content of metabolites. A mitogen-induced murine skin inflammation study suggested that alkamides were the active anti-inflammatory components present in Echinacea plants. Mixed alkamides and the major component, dodeca-2E,4E,8Z,10Z(E)-tetraenoic acid isobutylamides (8/9), were then isolated from E. purpurea root extracts for further bioactivity elucidation. In macrophages, the alkamides significantly inhibited cyclooxygenase 2 (COX-2) activity and the lipopolysaccharide-induced expression of COX-2, inducible nitric oxide synthase and specific cytokines or chemokines [i.e., TNF-α, interleukin (IL)-1α, IL-6, MCP-1, MIP-1β] but elevated heme oxygenase-1 protein expression. Cichoric acid, however, exhibited little or no effect. The results of high-performance liquid chromatography/electron spray ionization/mass spectrometry metabolite profiling of alkamides and phenolic compounds in E. purpurea roots showed that specific phytocompound (i.e., alkamides, cichoric acid and rutin) contents were subject to change under certain post-harvest or abiotic treatment. This study provides new insight in using the emerging metabolomics approach coupled with bioactivity assays for medicinal/nutritional plant species classification, quality control and the identification of novel botanical agents for inflammatory disorders.     

Creodonts and carnivores from the Middle Miocene Muruyur Formation at Kipsaraman and Cheparawa,Baringo District,Kenya

The Middle Miocene Muruyur Formation (ca 14.5 Ma), Tugen Hills, Kenya, has yielded a huge creodont and a variety of carnivores ranging in size from mongoose-sized viverrids and herpestids to lion-sized amphicyonids. The fauna partly fills what used to be a major gap in our knowledge of Neogene African carnivores, spanning the period between the better known Early Miocene assemblages of western Kenya and eastern Uganda, and the Late Miocene and Plio–Pleistocene faunas of East Africa. Present in the deposits are Megistotherium, two species of Hecubides, one species of Agnotherium, Herpestes, Vishnuictis, and one or two undetermined felids.     

Effects of different sex pheromone compositions and host plants on the mating behavior of two Grapholita species

The two congener species Grapholita molesta and Grapholita dimorpha share two major sex pheromone components: cis-8-dodecenyl acetate (Z8-12Ac) and trans-8-dodecenyl acetate (E8-12Ac). In fact, commercial sex pheromone lures composed of only these two major components attract the males of both species. In this study, we aimed to determine the reproductive isolation components of these two species by analyzing the effects of the minor sex pheromone components and host plants. First, different ratios of the two major sex pheromone components were greatly favored by either male species. Sex pheromone gland extracts of G. dimorpha contained a lesser proportion of Z8-12Ac than that of G. molesta. In the three (apple, pear, and peach) orchards investigated in this study, a larger number of G. molesta males were attracted to the 95:5 pheromone mixture (Z8-12Ac and E8-12Ac, respectively), while a larger number of G. dimorpha males were attracted to the 85:15 mixture. Second, there was a significant variation in male attractions in different host plants. G. molesta males were more attracted to the sex pheromone lure in the apple orchards than that in the pear and peach orchards. In contrast, G. dimorpha males were more attracted to the lures in the pear and peach orchards than that in the apple orchard. Third, the minor sex pheromone components were important for reproductive isolation. Among the four minor components tested, addition of (Z)-8-dodecenol (Z8-12OH) to the major sex pheromone components significantly suppressed male attraction in G. dimorpha and slightly elevated male attraction in G. molesta. The discriminating effect of Z8-12OH was further validated using male electroantennogram analysis. These results suggest that reproductive isolation between two congeners can be achieved by variations in the minor sex pheromone components and in the host plants, as well as by changes in the ratio of the two major components.