Phylogeny and biogeography of the pantropical genus Zanthoxylum and its closest relatives in the proto-Rutaceae group (Rutaceae)

The challenging biogeography of the Juan Fernández Islands and Coast Range of central Chile explained by new models of East Pacific tectonics

Biogeographers have often been puzzled by several unusual features in the Juan Fernández Islands (JFI) biota. These include the very high endemism density, multiple endemics that are older than the current islands, close biogeographic affinities with the central and West Pacific, and affinities with the diverse Coast Range of central Chile. We review aspects of biogeography in the JFI and the Coast Range in light of recent geological studies. These have examined the mantle below the East Pacific and South America, and have produced radical, new ideas on tectonic history. A long-lived, intraoceanic archipelago ~9000 km long is now thought to have existed in the East Pacific (passing between the JFI hotspot and mainland Chile) until the mid-Cretaceous. At this time, South America, which was moving westward with the opening of the Atlantic, collided with the archipelago. The assumption that the JFI biota is no older than its current islands is questionable, as taxa would have survived on prior islands produced at the JFI hotspot. We propose a new interpretation of evolution in the region based on tectonics rather than on island age and incorporating the following factors: the newly described East Pacific Archipelago; a long history for the JFI hotspot; metapopulation dynamics, including metapopulation vicariance; and formation of the Humboldt Current in the Cretaceous. The model accounts for many distinctive features of the JFI and Coast Range biota.

'Out of Africa' origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis

BACKGROUND AND AIMS

The staghorn fern genus Platycerium is one of the most commonly grown ornamental ferns, and it evolved to occupy a typical pantropical intercontinental disjunction. However, species-level relationships in the genus have not been well resolved, and the spatiotemporal evolutionary history of the genus also needs to be explored.

METHODS

Plastomes of all the 18 Platycerium species were newly sequenced. Using plastome data, we reconstructed the phylogenetic relationships among Polypodiaceae members with a focus on Platycerium species, and further conducted molecular dating and biogeographical analyses of the genus.

KEY RESULTS

The present analyses yielded a robustly supported phylogenetic hypothesis of Platycerium. Molecular dating results showed that Platycerium split from its sister genus Hovenkampia ~35.2 million years ago (Ma) near the Eocene-Oligocene boundary and began to diverge ~26.3 Ma during the late Oligocene, while multiple speciation events within Platycerium occurred during the middle to late Miocene. Biogeographical analysis suggested that Platycerium originated in tropical Africa and then dispersed eastward to southeast Asia-Australasia and westward to neotropical areas.

CONCLUSIONS

Our analyses using a plastid phylogenomic approach improved our understanding of the species-level relationships within Platycerium. The global climate changes of both the Late Oligocene Warming and the cooling following the mid-Miocene Climate Optimum may have promoted the speciation of Platycerium, and transoceanic long-distance dispersal is the most plausible explanation for the pantropical distribution of the genus today. Our study investigating the biogeographical history of Platycerium provides a case study not only for the formation of the pantropical intercontinental disjunction of this fern genus but also the 'out of Africa' origin of plant lineages.

Susceptibility of Tetranychus urticae to the Alkaloidal Extract of Zanthoxylum schreberi Bark: Phenotypic and Biochemical Insights for Biotechnological Exploitation

Tetranychus urticae Koch, a phytophagous mite, is one of the most significant crop pests globally. The primary method employed for controlling T. urticae involves chemical means, utilizing synthesized products, posing the risk of developing resistance. The urgency for novel strategies integrated into pest management programs to combat this mite is becoming increasingly imperative. Botanical pesticides emerge as a promising tool to forestall arthropod resistance. Among these, extracts from Rutaceae plants, abundant in bioactive specialized metabolites, have demonstrated potential as insecticides and miticides. In this study, various concentrations of alkaloidal extracts sourced from the bark of Zanthoxylum schreberi J.F.Gmel. (Rutaceae) were evaluated against T. urticae adult females. Furthermore, the extract's combination with three distinct commercial acaricides (i.e., chlorfenapyr, cyflumetofen, and abamectin) was also assessed for this mite. Chemical characterization of the extract via LC-MS allowed for the annotation of various compounds related to ten benzylisoquinoline-derived alkaloids. The extract, both alone and in combination with commercial insecticides, yielded varying responses, inducing over 40% mortality at 2% w/w, demonstrating a 90% repellency rate at the same concentration, and exerting a moderate impact on fecundity. These treatments extended beyond phenotypic responses, delving into the biochemical effects on treated T. urticae females through an exploration of the impact on four enzymes, i.e., acetylcholinesterase (AChE), glutathione S-transferase (GST), esterases (GE), and P450-like monooxygenases (PMO). Employing consensus docking studies and in vitro enzymatic evaluations, it was discovered that the Z. schreberi-derived extract and its constituents significantly affected two key enzymes, AChE and GST (IC50 < 6 µM), which were associated with the phenotypic observations of T. urticae females. The evaluation of alkaloid-rich botanicals showcases promising potential as a relevant biotechnological strategy in addressing mite-related concerns, offering a pathway toward innovative and sustainable pest management solutions.

Therapeutic Potential of the Genus Zanthoxylum Phytochemicals: A Theoretical ADME/Tox Analysis

Natural products (NPs) are essential in the search for new drugs to treat a wide range of diseases, including infectious and malignant disorders. However, despite the discovery of many bioactive NPs, they often do not make it to market as drugs due to toxicity and other challenges. The development of NPs into drugs is a long and expensive process, and many promising compounds are abandoned along the way. These molecules require in silico ADMET profiling in order to speed up their development into drugs lower costs, and the high attrition rate. The objective of this work was to produce thorough ADMET profiles of secondary metabolites from several classes that were isolated from Zanthoxylum species. The genus has a long history of therapeutic use, including treating tumours, hypertension, gonorrhoea, coughs, bilharzia, chest pains, and toothaches. The study used a dataset of 406 compounds from the genus for theoretical ADMET analysis. The findings revealed that 81% of the compounds met Lipinski's rule of five, indicating good oral bioavailability. The drug-likeness criteria were taken into account, with percentages ranging from 66.2 to 88.1 percent. Additionally, 9.2% of the compounds were predicted to be lead-like, demonstrating their potential as promising drug development candidates. Interestingly, none of the compounds inhibited hERG I, while 33% inhibited hERG II, potentially having cardiac implications. Additionally, 30% of the compounds exhibited AMES toxicity inhibition, while 23.6% were identified as hepatotoxic and 22.2% would cause skin sensitivity. Moreover, 81.8% of the compounds demonstrated high intestinal absorption, making them desirable for oral drugs. In conclusion, these findings highlight the diverse properties of the investigated compounds and their potential for drug development.

Leaf litter chemistry and its effects on soil microorganisms in different ages of Zanthoxylum planispinum var. Dintanensis

BACKGROUND

Leaf litter is the products of metabolism during the growth and development of plantation, and it is also an important component of nutrient cycling in plantation ecosystems. However, leaf litter chemistry and its effects on soil microorganisms in different ages, as well as the interactions between chemical components in leaf litter have been rarely reported. Based on this, this paper took Zanthoxylum planispinum var. dintanensis (hereafter Z. planispinum) plantations of 5-7, 10-12, 20-22, and 28-32 years old as the objects. By using one-way ANOVA, Pearson correlation analysis and redundancy analysis, we investigated leaf litter chemistry and its effects on soil microorganisms in different ages, and to reveal internal correlation of various chemical components in leaf litter, which can provide a scientific basis for the regulation of soil microbial activity in plantations.

RESULTS

The variation of organic carbon with plantation age was more stable compared to total nitrogen and phosphorus of leaf litter. Nitrogen resorption was stronger than phosphorus resorption efficiency in Z. planispinum, and resorption efficiencies of leaf nitrogen and phosphorus for different ages were lower than the global average. Total nitrogen was highly significantly positively correlated with lignin, and total potassium was significantly positively correlated with tannin, suggesting the increase of inorganic substances in leaf litter would promote the accumulation of secondary metabolites. The leaf litter chemical traits explained up to 72% of soil microorganisms, where lignin was positively correlated with fungi and negatively correlated with bacteria, indicating that fungi are able to decompose lower quality litter and can break down complex and stable organic compounds more rapidly than bacteria. The nutrient elements carbon and nitrogen in the leaf litter and their interrelationship also have a great impact on soil microorganisms, because carbon is not only the element that provides energy, but also the element with the largest content in the microbiota.

CONCLUSIONS

The sustained increase in inorganic nutrients of leaf litter did not favor the decomposition of secondary metabolites, but rather inhibited the degradation of leaf litter. The significant positive effect of the leaf litter chemistry on soil microorganisms indicates the important role of leaf litter in promoting nutrient cycling in Z. planispinum plantations.

Ethnobotanical uses, phytochemistry and pharmacology of pantropical genus Zanthoxylum L. (Rutaceae): An update

ETHNOPHARMACOLOGICAL RELEVANCE

Plants have been used in various parts of the world to treat various diseases. The genus Zanthoxylum L. (Rutaceae) is the second largest genus of this family and comprises approximately 225-549 species distributed in the tropical and temperate regions of the world. Plants of this genus are trees and shrubs with various applications in folklore medicine for food, medicine, construction, and other uses.

AIM OF THE REVIEW

The goal of this review is to give an updated data on the ethnobotanical applications, phytochemistry, and pharmacology of the Zanthoxylum species to investigate their medicinal potential and identify research gaps for future research studies.

MATERIALS AND METHODS

Data was obtained through a systematic search of published literature and online databases such as Google Scholar, Web of Science, PubMed, Science Direct, and Sci-Finder. The botanical names were confirmed using the World Flora Online and chemical structures were drawn using the ChemBio Draw Ultra Version 14.0 Software.

RESULTS

The Zanthoxylum species have a wide use in different parts of the continents as a remedy for various diseases such as digestive diseases, gastrointestinal disorders, venereal diseases, respiratory diseases, rheumatism, bacterial diseases, viral, and other diseases. Various parts of the plant comprising fruits, seeds, twigs, leaves, oils, and stems are administered singly or in the form of decoction, infusion, powder, paste, poultice, juice, or mixed with other medicinal plants to cure the disease. More than 400 secondary metabolites have been isolated and characterized in this genus with various biological activities, which comprise alkaloids, flavonoids, coumarins, lignans, alcohols, fatty acids, amides, sesquiterpenes, monoterpenes, and hydrocarbons. The crude extracts, fractions, and chemical compounds isolated from the genus have demonstrated a wide range of biological activities both in vivo and in vitro, including; anti-cancer, antimicrobial, anti-sickling, hepatoprotective, antipyretic, antitumor, and other pharmacological activities.

CONCLUSION

This genus has demonstrated an array of phytoconstituents with therapeutic potential. The ethnobotanical uses of this genus have been confirmed in modern pharmacological research. This genus is a potential source for modern drug discovery and health care products. Further and extensive research is therefore required on the safety approval and therapeutic application of the species of this genus as well as clinical trials and pharmacokinetic studies.

A versatile untargeted metabolomics-driven technology for rapid phytochemical profiling of stem barks of Zanthoxylum species with antioxidant and antimicrobial activities

Zanthoxylum species are credited with various uses in ethnomedicine due to their rich metabolite composition. In Kenya, these include management of cancer and microbial related ailments. However, there are limited reports showing how the bioactivity of Kenyan Zanthoxylum species is linked to their phytochemical profiles. This study therefore aimed at examining the chemical variation among five Zanthoxylum species found in Kenya (Z. chalybeum, Z. gilletii, Z. holtzianum, Z. paracanthum and Z. usambarense) using metabolomics approaches and the anti-oxidant and antimicrobial activities of these species. In a Folin–Ciocalteu test, the phenolic content of the stem bark extracts of these species were 73.083–145.272 mg TAE/g, while the alkaloids (in bromothymol blue chromogenic test) and flavonoids (in aluminium chloride test) were found to be 152.39–207.19 mg ME/g, and 109.416–186.413 mg CE/g, respectively. These extracts also exerted strong antioxidant activities in the 2,2-iphenyl-1-picrylhydrazyl (DPPH) and ferric ion reducing antioxidant power assays. In a broth dilution assay, the extract of the stem bark of Z. holtzianum ability showed the highest antimicrobial activity, followed by Z. chalybeum stem bark extract. The activities were positively correlated to both flavonoids and alkaloids concentrations, while the concentration of phenolics had weak negative correlation to antimicrobial activities. A chemometric analysis of the liquid-chromatography mass spectrometry profiles led to grouping of the species into three clusters. This study illustrates the variation in the bioactivity of Zanthoxylum species based on metabolite composition and justifies the wide usage of Zanthoxylum species in Kenyan traditional medicinal practices.

Graphical abstract

The complete chloroplast genome of Zanthoxylum stenophyllum Hemsl. (Rutaceae), a traditional Chinese medicinal plant

Zanthoxylum stenophyllum Hemsl., a type species for the genus Zanthoxylum (Rutaceae), is a traditional medicinal plant. We studied the complete chloroplast genome of this species using BGISEQ-500 platform. The chloroplast genome was 158,314 bp in size with a GC content of 38.45%. The genome contained two short inverted repeat (IRa and IRb) regions of 27,052 bp, a large single-copy region (LSC, 86,029 bp) and a small single-copy region (SSC, 18,181 bp). The annotated complete chloroplast genome contains 133 distinct genes, including 88 protein-coding genes, 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Phylogenetic analysis indicated that Z. stenophyllum is clustered with Z. schiniflium and Z. pinnatum in the same branch with 100% bootstrap support. This complete chloroplast genome provides valuable genomic information for the molecular phylogeny and sustainable utilization of Zanthoxylum.

Characterization of the complete chloroplast genome of Zanthoxylum esquirolii Levl. (Rutaceae)

Zanthoxylum esquirolii Léveillé 1914 is mainly distributed in southwest China, and its wild germplasm resources are scarce and in urgent need of conservation. In this study, we report the first complete chloroplast genome sequence of Z. esquirolii using next-generation sequencing. The circular genome is 158,390 bp in length, containing two inverted repeat (IR) regions of 27,622 bp separated by a large single copy (LSC) region of 85,580 bp and a small single copy (SSC) region of 17,566 bp. The chloroplast genome contains a total of 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome was 38.46%, with corresponding values in the LSC, SSC, and IR regions of 36.84%, 33.55%, and 42.51%, respectively. The phylogenetic tree revealed that Z. esquirolii Levl. formed a clade with Z. piperitum DC., Z. bungeanum Maxim., Z. simulans Hance and Z. sp. NH-2018, and had a strongly supported sister relationship with Z. bungeanum.

Combined morphological and multi-omics analyses to reveal the developmental mechanism of Zanthoxylum bungeanum prickles

Zanthoxylum bungeanum Maxim. as an important economic forest, its epidermis bears prickles which complicate the harvesting process and increase the labor costs. To explore the developmental mechanism of prickles, three varieties of Zanthoxylum bungeanum (PZB, SZB, GSZB) were selected for morphological and multi-omics analyses. The absorption spectra of prickles and stems were detected using Fourier-transform infrared spectroscopy (FTIR), and they were found different at 1617, 1110, 3319, and 1999 cm^-1. The morphology of prickles and stems were observed using light microscopy and transmission electron microscopy (TEM). The growth direction of cells on the prickle side and stem side were perpendicular to each other, and there was a resembling abscission zone (RAZ) between them. The vacuolar deposits of prickle cells were much more than stem cells, indicating that the lignification degree of prickles was higher than stems. In addition, 9 candidate genes (ZbYABBY2, ZbYABBY1, ZbYABBY5, ZbWRKY, ZbLOG5, ZbAZG2, ZbGh16, ZbIAA33, and ZbGh16X1) were screened out and validated base on transcriptome and qRT-PCA. As well as, 30 key metabolites were found related to prickle development base on metabolome analysis. Among them, 4-hydroxy-2-oxopentanoate, trans-2-hydroxy-cinnamate, trans-cinnamate, polyhydroxy-fatty acid, 10,16-dihydroxypalmitate, cinnamic acid were related to the biosynthesis of cutin, suberine and wax. Indole-3-acetate, tryptamine, anthranilate, fromylanthranilate, N6-(delta2-isopentenyl)-adenine were related to plant hormone signal transduction. Generally, this is the first study to reveal the developmental mechanism of prickles. The results of this study lay the foundation for the breeding of non-prickle Zanthoxylum bungeanum.

Evaluating the Impacts of Climate Factors and Flavonoids Content on Chinese Prickly Ash Peel Color Based on HPLC-MS and Structural Equation Model

Climate affects Chinese prickly ash peel color directly through temperature and illumination and indirectly influences it through its effect on flavonoid compounds. In this study, a comprehensive evaluation strategy based on high performance liquid chromatography-mass spectrometry (HPLC-MS) technology and a structural equation model was applied to evaluate the effects of climate factors and flavonoids on Chinese prickly ash peel color. There were obvious geographical variations of peel color and flavonoid compounds with an obvious east–west distribution trend which were divided into high-altitude type and low-altitude type. Through path analysis, the wind speed, temperature and annual sunshine duration were found to be the key environmental factors affecting the flavonoids content and peel color, and their direct effects were higher than their indirect effect. Based on HPLC-MS technology and a structural equation model, correlation models of climatic factors and flavonoids with peel color were established, and the factors that had greater weight on pericarp color were obtained. Our results provide experimental evidence that climate factors affect the peel color by affecting flavonoid biosynthesis and accumulation, reveal the geographical variation of peel color and flavonoid component contents in Chinese prickly ash peel, establish a quantization color method for rapid evaluation of peel quality, expand on the influence of climatic factors on flavonoids content and peel coloration and promote agricultural practice in areas with similar climatic conditions.

Taxonomic delimitation and molecular identification of clusters within the species Zanthoxylumnitidum (Rutaceae) in China

Zanthoxylumnitidum, known as Liang-Mian-Zhen in China, is a traditional Chinese medicinal plant used to treat traumatic injury, rheumatism, paralysis, toothache, stomach ache, and venomous snake bites. Two varieties of the species have been described and three morphological types have been reported within the original variety. However, taxonomic delimitation and molecular markers for distinguishing these varieties and types within this species remain unknown. Since different populations exhibit varying chemical compositions, easy identification of intraspecific taxa is crucial. We collected 420 individuals from 38 natural populations, 3 samples of standard medicinal material, and 17 folk-medicine samples to perform classification and identification within Zanthoxylumnitidum. Four distinct genetic clusters (A, B, C, and D) were highly supported by the nuclear barcode. Two distinct chloroplast clusters (A1 and A2) were further detected within A, and three others had one-to-one correspondence with the remaining nuclear clusters. Molecular identification showed that the 17 folk samples comprised A1, A2, B, and D, while the 3 standard samples belonged to A2. The internal transcribed spacer (ITS) region and rbcL gene are proposed as barcodes for rapid and accurate identification of the different Liang-Mian-Zhen lineages in China. This study highlights the importance of accurate taxonomic delimitation in combination with rapid and accurate molecular identification of medicinal plants.

The complete chloroplast genome sequence of Zanthoxylum undulatifolium Hemsl. (Rutaceae)

Zanthoxylum undulatifolium is an excellent economic tree species with important medical value. This study reports the first complete chloroplast genome sequence of Z. undulatifolium. Its whole chloroplast genome is 158,400 bp in length, including a large single-copy (LSC) region of 85,898 bp, a small single-copy (SSC) region of 17,610 bp, and two inverted repeat (IR) regions of 27,446 bp. The chloroplast genome contains a total of 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome is 38.46%, with the corresponding values in the LSC, SSC, and IR regions are 36.87%, 33.51%, and 42.55%, respectively. Phylogenetic analysis revealed the sister relationship between Z. undulatifolium and Z. bungeanum.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.

Transcriptome analysis reveals the molecular mechanisms of response to an emergent yellow-flower disease in green Chinese prickly ash (Zanthoxylum schinifolium)

Chinese prickly ash (Zanthoxylum) is extensively used as spice and traditional medicine in eastern Asian countries. Recently, an emergent yellow-flower disease (YFD) break out in green Chinese prickly ash (Zanthoxylum schinifolium, Qinghuajiao in Chinese) at Chongqing municipality, and then leads to a sharp reduction in the yield of Qinghuajiao, and thus results in great economic losses for farmers. To address the molecular response for the emergent YFD of Qinghuajiao, we analyzed the transcriptome of 12 samples including the leaves and inflorescences of asymptomatic and symptomatic plants from three different towns at Chongqing by high-throughput RNA-Seq technique. A total of 126,550 genes and 229,643 transcripts were obtained, and 21,054 unigenes were expressed in all 12 samples. There were 56 and 164 different expressed genes (DEGs) for the AL_vs_SL (asymptomatic leaf vs symptomatic leaf) and AF_vs_SF (asymptomatic flower vs symptomatic flower) groups, respectively. The results of KEGG analysis showed that the “phenylpropanoid biosynthesis” pathway that related to plant–pathogen interaction were found in AL_vs_SL and AF_vs_SF groups, and the “Plant–pathogen interaction” found in AF_vs_SF group, implying that this Qinghuajiao YFD might cause by plant pathogen. Interestingly, we detected 33 common unigenes for the 2 groups, and almost these unigenes were up-regulated in the symptomatic plants. Moreover, most of which were homologs to virus RNA, the components of viruses, implying that this YFD was related to virus. Our results provided a primary molecular basis for the prevention and treatment of YFD of Qinghuajiao trees.

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.

METHODS

A 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 RESULTS

Four 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.

CONCLUSIONS

Target 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.

Characterization of the complete chloroplast genome of Toddalia asiatica (L.) Lam

Toddalia asiatica (L.) Lam. belongs to family Rutaceae and mainly distributes in dry areas of bushes in tropical Africa, Asia, and Swaziland. Sometimes it can be used as fodder for goats, but it has been used as herbs in traditional medical treatment for 1000 years. In this study, we sequenced the sample of T. asiatica and determined its complete chloroplast genome. The length of CP genome is 158,434 bp, includes two invert repeats (IR) regions of 27,008 bp, a large single-copy (LSC) region of 86,132 bp, and a short single-copy (SSC) region of 18,286 bp. There are 133 genes, which includes 88 protein-coding genes, 8 rRNA and 37 tRNA, and 38.5% overall GC content. Each of trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA genes contains a intron, clpP and ycf3 contains 2 intron. The phylogenetic analysis result shows that T. asiatica has the closest relationship with Zanthoxylum armatum (MT990984) and Zanthoxylum nitidum (MN508801).

Cytotoxic alkaloids from the root of Zanthoxylum paracanthum (mildbr) Kokwaro

Chemical investigation of the root of Zanthoxylum paracanthum afforded 1 new alkamide derivative, (2E,4E)-6-oxo-N-isobutyldeca-2,4-dienamide (1) together with 10 known congeners including one phenolic amide (2), four benzophenanthridines (3 - 6), three indolonaphthyridines (7 - 9) and two lignans (10 and 11). Their structures were elucidated by a combination of spectroscopic and spectrometric data. Using resazurin reduction assay, the crude extract (10 µg/mL) and isolates (10 µM) were screened for their cytotoxic activities against the drug-sensitive (CCRF-CEM) leukemia cell line and its multidrug-resistant counterpart (CEM/ADR5000). Compounds 3, 4 and 6 showed cytotoxicity against CCRF-CEM with IC₅₀ values of 2.00 ± 0.33, 2.31 ± 0.20 and 0.11 ± 0.04 µM, respectively. Only compound 6 exhibited strong cytotoxic activity against CEM/ADR5000 with an IC₅₀ value of 2.34 ± 0.34 µM in comparison with the standard drug doxorubicin which showed IC₅₀ values of 0.01 ± 0.14 (CCRF-CEM) and 26.78 ± 3.30 µM (CEM/ADR5000).

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq

Japanese pepper, Zanthoxylum piperitum, is native to Japan and has four well-known lineages (Asakura, Takahara, Budou, and Arima), which are named after their production area or morphology. Restriction-site associated DNA sequencing (RAD-Seq) was used to analyse 93 accessions from various areas, including these four lineages. Single nucleotide variant analysis was used to classify the plants into eight groups: the Asakura and Arima lineages each had two groups, the Takahara and Budou lineages each had one group, and two additional groups were present. In one Asakura group and two Arima groups, the plants were present in agricultural fields and mountains, thus representing the early stage of domestication of the Japanese pepper. The second Asakura lineage group was closely related to plants present in various areas, and this represents the second stage of domestication of this plant because, after early domestication, genetically related lineages with desirable traits spread to the periphery. These results demonstrate that domestication of Japanese pepper is ongoing. In addition, this study shows that spineless plants are polyphyletic, despite the spineless lineage being considered a subspecies of Japanese pepper.

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

The complete chloroplast genome of Phellodendron chinense (Rutaceae), an Endangered medicinal plant in southern China

Phellodendron chinense is an Endangered medicinal plant in southern China. In this study, the complete chloroplast genome sequence of P.chinense was characterized by de novo assembly. The length of the whole chloroplast genome was 158,537 bp, containing a large single copy region (LSC) of 86,250 bp and a small single copy region (SSC) of 18,287 bp, which were separated by a pair of 27,000 bp inverted repeat regions (IRs). The sequence contains 114 unique genes, including 30 tRNA, 4 rRNA, and 80 protein-coding genes. The overall GC content of the chloroplast genome is 38.4% and those in the LSC, SSC, and IR regions are 36.6, 33.2, and 42.9%, respectively. The phylogenetic analysis based on reported chloroplast sequences of Rutaceae showed that P. chinense is sister to P. amurense, consisting a monophyletic group, and that Phellodendron is closely related to Zanthoxylum.

Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic

Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

Background

Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.

Results

Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage).

Conclusions

The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.

Development and Application of InDel Markers for Authentication of the Korean Herbs Zanthoxylum schinifolium and Zanthoxylum piperitum

Zanthoxylum schinifolium and Zanthoxylum piperitum are the sources of the well-known traditional Korean herbal medicines “sancho” (prickly ash) and “chopi” (Korean pepper), respectively. Sancho and chopi are often indiscriminately mixed due to the similar appearance of the herbal materials when used as spices and herbal medicines. Moreover, commercial sancho and chopi products often contain adulterants, which is insufficient to ensure food efficacy and safety. In this study, we developed hypervariable insertion/deletion (InDel) markers to distinguish between sancho and chopi products by comparing the complete chloroplast genome sequences of four Zanthoxylum species deposited in the National Center for Biotechnology Information (NCBI) GenBank. Comparative analyses of the nucleotide diversity (Pi) of these Zanthoxylum genomes revealed four hypervariable divergent sites (trnH-psbA, psbZ-trnG, trnfM-rps14, and trnF-ndhK) with Pi > 0.025 among 520 windows. Of these four regions, including two genic and two intergenic regions, only psbZ-trnG yielded accurate PCR amplification results between commercial sancho and chopi products from the Korean herbal medicine market. We therefore selected psbZ-trnG, an InDel-variable locus with high discriminatory powers, as a candidate DNA barcode locus. This InDel marker could be used as a valuable, simple, and efficient tool for identifying these medicinal herbs, thereby increasing the safety of these spices and herbal materials in the food market.

History and Geography of Neotropical Tree Diversity

Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.

In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation

In liquid chromatography-mass spectrometry (LC-MS) metabolomics, data matrices with up to thousands of variables for each ion peak are subjected to multivariate analysis (MVA) to assess the homogeneity between samples. The large dimensions of LC/MS datasets hinder the identification of the discriminant or the metabolic markers. In the present study, the molecular network (MN) approach and two in silico annotation tools, network annotation propagation (NAP) and the hierarchical chemical classification method, ClassyFire, were used to annotate the metabolites of three Zanthoxylum species, Z. bungeanum, Z. schinifolium and Z. piperitum. The in silico annotation results of the MN nodes and the MVA variables were combined and visualized in loading plots. This approach helped intuitive detection of the variables that greatly contributed to the separation of the samples in the score plot as discriminant or metabolic markers, thereby allowing rapid annotation of two flavanone derivatives.

Morphological and Molecular Characterization of Zanthoxylum zanthoxyloides (Rutaceae) from Burkina Faso

Zanthoxylum zanthoxyloides is a West African forest tree that is used for example against malaria and sickle cell anemia in Burkina Faso. The goal of this study was to analyze the genetic and morphological diversity of the species within wild populations in Burkina Faso, where it is potentially under threat due to the uncontrolled harvesting of its roots. Seventy-two trees from three different sites in Southwestern Burkina Faso were analyzed. Each tree was characterized by 12 traits specifying the period of flowering and maturity as well as morphological characteristics of the stem, leaves, and seeds. The molecular analysis was performed using two plastid DNA regions (psbA-trnH and trnL-trnF) and two nuclear regions (GBSSI and ITS) to identify the genetic diversity of the species for further development of a management plan for ex situ reproduction and in situ conservation. We found variability in morphological traits correlating with the geographic distance of the study sites. The molecular analysis, in contrast, revealed hardly any genetic variability among the tested trees and no population structure. Whether the differences in morphological traits are caused by different environmental conditions or by genetic variability in genes linked to morphological traits needs further testing. The apparent lack of genetic differentiation suggests that germplasm throughout the study region is suitable for planting in conservation actions. Efficient conservation management should involve local communities, especially those interested in traditional medicine.

Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression

Hawaiian Melicope are one of the major adaptive radiations of the Hawaiian Islands comprising 54 endemic species. The lineage is monophyletic with an estimated crown age predating the rise of the current high islands. Phylogenetic inference based on Sanger sequencing has not been sufficient to resolve species or deeper level relationships. Here, we apply restriction site-associated DNA sequencing (RAD-seq) to the lineage to infer phylogenetic relationships. We employ Quartet Sampling to assess information content and statistical support, and to quantify discordance as well as partitioned ABBA-BABA tests to uncover evidence of introgression. Our new results drastically improved resolution of relationships within Hawaiian Melicope. The lineage is divided into five fully supported main clades, two of which correspond to morphologically circumscribed infrageneric groups. We provide evidence for both ancestral and current hybridization events. We confirm the necessity for a taxonomic revision of the Melicope section Pelea, as well as a re-evaluation of several species complexes by combining genomic and morphological data.

Insecticidal and repellent efficacy against stored-product insects of oxygenated monoterpenes and 2-dodecanone of the essential oil from Zanthoxylum planispinum var. dintanensis

Essential oils (EOs) extracted from leaves (EL) and fruit pericarp (EFP) of Zanthoxylum planispinum var. dintanensis were analyzed for their chemical composition by GC-MS technique and evaluated for their fumigant, contact toxicity and repellency against three stored-product insects, namely Tribolium castaneum, Lasioderma serricorne, and Liposcelis bostrychophila adults. Results of GC-MS analysis manifested that EL and EFP of Z. planispinum var. dintanensis were mainly composed of oxygenated monoterpenes. Major components included linalool, sylvestrene and terpinen-4-ol. The obvious variation observed between two oil samples was that EL contained 2-dodecanone (11.52%) in addition to the above mentioned components, while this constituent was not detected in EFP. Bioassays of insecticidal and repellent activities were performed for EL, EFP as well as some of their individual compounds (linalool, terpinen-4-ol and 2-dodecanone). Testing results indicated that EL, EFP, linalool, terpinen-4-ol and 2-dodecanone exhibited potent insecticidal and repellent activities against the three target insects selected. Among the three individual compounds, 2-dodecanone was significantly toxic to T. castaneum (LD₅₀ = 5.21 μg/adult), L. serricorne (LD₅₀ = 2.54 μg/adult) and L. bostrychophila (LD₅₀ = 23.41 μg/cm²) in contact assays and had beneficial repellent effects on L. serricorne at 2 and 4 h post-exposure. The anti-insect efficacy of Z. planispinum var. dintanensis EO suggests it has potential to be used as botanical insecticide or repellent to control pest damage in warehouses and grain stores.

Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper (Zanthoxylum Armatum) by Virome Analysis

An emerging virus-like flower yellowing disease (FYD) of green Sichuan pepper (Zanthoxylum armatum v. novemfolius) has been recently reported. Four new RNA viruses were discovered in the FYD-affected plant by the virome analysis using high-throughput sequencing of transcriptome and small RNAs. The complete genomes were determined, and based on the sequence and phylogenetic analysis, they are considered to be new members of the genera Nepovirus (Secoviridae), Idaeovirus (unassigned), Enamovirus (Luteoviridae), and Nucleorhabdovirus (Rhabdoviridae), respectively. Therefore, the tentative names corresponding to these viruses are green Sichuan pepper-nepovirus (GSPNeV), -idaeovirus (GSPIV), -enamovirus (GSPEV), and -nucleorhabdovirus (GSPNuV). The viral population analysis showed that GSPNeV and GSPIV were dominant in the virome. The small RNA profiles of these viruses are in accordance with the typical virus-plant interaction model for Arabidopsis thaliana. Rapid and sensitive RT-PCR assays were developed for viral detection, and used to access the geographical distributions. The results revealed a correlation between GSPNeV and the FYD. The viruses pose potential threats to the normal production of green Sichuan pepper in the affected areas due to their natural transmission and wide spread in fields. Collectively, our results provide useful information regarding taxonomy, transmission and pathogenicity of the viruses as well as management of the FYD.

Maternal mitochondrial inheritance in two Fusarium pathogens of prickly ash (Zanthoxylum bungeanum) in northern China

Mitochondrial inheritance in Fusarium zanthoxyli and F. continuum, two canker-inducing pathogens of prickly ash (Zanthoxylum bungeanum) in northern China, was investigated by genotyping ascospore progeny obtained from laboratory crosses. Polymorphic regions of the mitochondrial genomes (mitogenomes) that contained indels and single-nucleotide polymorphisms (SNPs) were identified via comparative analyses of the complete mitogenomes of the parents used in the intraspecific crosses. A reciprocal genetic cross of F. zanthoxyli NRRL 66714 × NRRL 66285, and a separate cross of F. continuum ♀ NRRL 66286 × ♂ NRRL 66218, revealed that mitochondria were only inherited from the maternal parent. In addition, the reciprocal cross demonstrated that mitochondrial inheritance is not linked to mating type. Gene order in the circular mitogenomes of the prickly ash pathogens was identical to that previously reported for other fusaria and members of the Hypocreales, except that the TRNL tRNAs were duplicated in F. zanthoxyli NRRL 66714. The genomes contained 14 polypeptide-encoding genes involved in oxidative respiration, one intron-encoded ribosomal protein (rps3) gene, two ribosomal RNA (rRNA) genes, and 26-28 tRNA genes. The F. zanthoxyli mitogenomes were 80.9 and 98.7 kb in length, whereas those of F. continuum were considerably shorter and nearly identical in length at 63.4 kb. The significant differences in mitogenome length were primarily due to variable numbers of introns and open reading frames (ORFs) encoding hypothetical proteins.