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Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila , a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila , and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin. Ophiorrhiza pumila is a medicinal plant that can produce the anti-cancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.

Background Starting from the ancient time, the people of Ethiopia use medicinal plants as traditional medicine to heal different human and livestock ailments. This ethnobotanical study of medicinal plants was carried out in Ganta Afeshum District, Eastern Zone of Tigray, Northern Ethiopia, to identify medicinal plant species used by the local community to treat various human and livestock ailments. Methods A total of 78 informants (54 men and 24 women) were selected to collect ethnobotanical information from four study sites. Among the 78 informants, 20 key informants were selected purposefully; the other 58 informants were selected randomly by lottery method. Ethnobotanical data were collected using semi-structured interviews, field observations, guided field walks, and group discussions and were analyzed by preference ranking, paired comparison, direct matrix ranking, informant consensus factor, fidelity level (FL), use-value, independent samples t test, and Pearson correlation coefficients. Results A total of 173 medicinal plants were collected and identified that were distributed across 77 families and 156 genera. The family Fabaceae stood first by contributing 17 (9.8%) species followed by Lamiaceae and Solanaceae with 9 (5.2%) species each. Rhamnus prinoides was reported for the treatment of many of the described diseases. One hundred sixteen (67.1%) medicinal plant species were collected from natural vegetation, 34 (19.7) were from home gardens, 13 (7.5%) from farmland, and 10 (5.8%) were from natural vegetation and home gardens. The most widely used life form was herbs (69 species, 39.9%) followed by shrubs (58 species, 33.5%). The most commonly used part of the medicinal plants was the leaves followed by roots. The plants were prepared by grinding, powdering, squeezing, roasting, and burning and were administered through oral, dermal, nasal, anal, ocular, and vaginal, and on the surface of the teeth. The most commonly used applications were by drinking, smearing, eating, fumigation, and chewing. There was no difference between men and women informants, showing that the two sexes had similar knowledge in the use of traditional medicinal plants. Educational level and medicinal plant knowledge of informants were negatively correlated; whereas age and medicinal plant knowledge of informants were positively correlated. Conclusions Ganta Afeshum District is relatively rich in diversity of medicinal plant resources accompanied with a rich indigenous knowledge within the local communities to harvest and effectively use to prevent different human and livestock ailments. However, nowadays, deforestation, agricultural expansion, overgrazing, drought, and overexploitation are threatening these properties. Therefore, people of the study area should apply complementary conservation approaches (in situ and ex situ) for sustainable use of these resources and to prevent species extinction.

Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus , a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway. The medicinal plant Catharanthus roseus is a source of leading anticancer drugs. The monoterpene indole alkaloid (MIA) biosynthetic pathway in C. roseus has now been analyzed using a complementary, multi-omics, single-cell approach. This identified clusters of genes involved in MIA biosynthesis and cell-type-specific partitioning in the MIA biosynthetic pathway.

Selecting candidates for drug developments using computational design and empirical rules has resulted in a broad discussion about their success. In a previous study, we had shown that a species’ abundance [as expressed by the GBIF (Global Biodiversity Information Facility)] dataset is a core determinant for the development of a natural product into a medicine. Our overarching aim is to understand the unique requirements for natural product-based drug development. Web of Science was queried for research on alkaloids in combination with plant systematics/taxonomy. All alkaloids containing species demonstrated an average increase of 8.66 in GBIF occurrences between 2014 and 2020. Medicinal Species with alkaloids show higher abundance compared to non-medicinal alkaloids, often linked also to cultivation. Alkaloids with high biodiversity are often simple alkaloids found in multiple species with the presence of ’driver species‘ and are more likely to be included in early-stage drug development compared to ‘rare’ alkaloids. Similarly, the success of an alkaloid containing species as a food supplement (‘botanical’) is linked to its abundance. GBIF is a useful tool for assessing the druggability of a compound from a certain source species. The success of any development programme from natural sources must take sustainable sourcing into account right from the start.

Background The present study is the first quantitative ethnobotanical evaluation of Harighal, an inaccessible and unexplored area of District Bagh Azad Jammu & Kashmir (AJK). The exploration, quantification, and comparison of ethnobotanical knowledge among different rural communities of the study area were mainly focused during field survey. Methodology In total, 79 informants (49 men and 34 women) were selected randomly to collect data using a semi-structured questionnaire. Various quantitative indices, including use value, relative frequency of citation, relative importance, fidelity level, and informant consent factor, were employed to evaluate the gathered information. Furthermore, primary data were also compared with twenty-two papers published from adjoining areas. Result A total of 150 medicinal plants belonging to 98 genera and 60 families were documented. Asteraceae, Fabaceae, and Rosaceae were the dominant families having 15 species each. Of these, 76 species were indigenous, 74 exotic, 136 were collected in the wild, 10 cultivated, and 4 both wild-collected and cultivated. Herbaceous taxa were the most used life form, and leaves were the most exploited plant part. Decoctions were the most preferred method used in preparation of herbal recipes. Three species viz. Mentha longifolia , Berberis lycium , and Galium aparine had the highest use value (1.05), relative frequency of citation (0.81), and relative importance value (96), respectively. The highest informant consensus factor (ICF) was reported for digestive disorders. Mentha longifolia , Punica granatum , Zanthoxylum alatum , and Olea ferruginea had 100% fidelity values. The Jaccard index revealed that uses of plants were more similar in two neighboring areas, i.e., Pearl Valley and Toli Peer. Conclusion Local inhabitants still prioritize herbal medicines as an effective way to treat a wide variety of ailments. Elders and health practitioners of the study area are well aware of indigenous knowledge about medicinal plants, but young people are not much interested in herbal practices. Thus, valuable knowledge about the use of plants is on the verge of decline.

This paper presents the first quantitative ethnobotanical study of the flora in Toli Peer National Park of Azad Jammu and Kashmir, Pakistan. Being a remote area, there is a strong dependence by local people on ethnobotanical practices. Thus, we attempted to record the folk uses of the native plants of the area with a view to acknowledging and documenting the ethnobotanical knowledge. The aims of the study were to compile an inventory of the medicinal plants in the study area and to record the methods by which herbal drugs were prepared and administered. Information on the therapeutic properties of medicinal plants was collected from 64 local inhabitants and herbalists using open ended and semi-structured questionnaires over the period Aug 2013-Jul 2014. The data were recorded into a synoptic table comprising an ethnobotanical inventory of plants, the parts used, therapeutic indications and modes of application or administration. Different ethnobotanical indices i.e. relative frequencies of citation (RFC), relative importance (RI), use value (UV) and informant consensus factor (Fic), were calculated for each of the recorded medicinal plants. In addition, a correlation analysis was performed using SPSS ver. 16 to check the level of association between use value and relative frequency of citation. A total of 121 species of medicinal plants belonging to 57 families and 98 genera were recorded. The study area was dominated by herbaceous species (48%) with leaves (41%) as the most exploited plant part. The Lamiaceae and Rosaceae (9% each) were the dominant families in the study area. Among different methods of preparation, the most frequently used method was decoction (26 species) of different plant parts followed by use as juice and powder (24 species each), paste (22 species), chewing (16 species), extract (11 species), infusion (10 species) and poultice (8 species). The maximum Informant consensus factor (Fic) value was for gastro-intestinal, parasitic and hepatobiliary complaints (0.90). Berberis lycium Ajuga bracteosa, Prunella vulgaris, Adiantum capillus-veneris, Desmodium polycarpum, Pinus roxburgii, Albizia lebbeck, Cedrella serrata, Rosa brunonii, Punica granatum, Jasminum mesnyi and Zanthoxylum armatum were the most valuable plants with the highest UV, RFC and relative importance values. The Pearson correlation coefficient between UV and RFC (0.881) reflects a significant positive correlation between the use value and relative frequency of citation. The coefficient of determination indicated that 77% of the variability in UV could be explained in terms of RFC. Systematic documentation of the medicinal plants in the Toli Peer National Park shows that the area is rich in plants with ethnomedicinal value and that the inhabitants of the area have significant knowledge about the use of such plants with herbal drugs commonly used to cure infirmities. The results of this study indicate that carrying out subsequent pharmacological and phytochemical investigations in this part of Pakistan could lead to new drug discoveries.

Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.