Indigenous knowledge and quantitative ethnobotany of the Tanawal area, Lesser Western Himalayas, Pakistan.

Ethnobotanical field surveys were carried out in the Tanawal area of the Lesser Himalayan Region, Khyber Pakhtunkhawa, Province from April 2016 to October 2017. The area is located between 34.36 (34° 21' 30 N) latitude and 73.07 (73° 4' 0 E) longitude with an average elevation of 1374 meters above sea level. Ethnomedicinal data were collected through Participatory Rural Appraisal (PRA), and participants were selected through the snow-boll technique. Semi-structured, in-depth and open-ended interviews were conducted. The data were quantitatively evaluated using ethnomedicinal indices i.e. Relative frequency of citation (RFCs), Fidelity level (FL), and Use Value (UV). The ethnobotanical data were also comparatively analyzed through the Jaccard Index (JI). The study yielded 66 medicinal plants in 62 genera and 43 families. Asteraceae and Solanaceae were the most important families with five medicinal taxa each. Regarding medicinal plant part utilization, leaves (43.28%) were used predominantly, followed by whole plant (14.92%) and fruits (14.92%). Decoction was the main drug formulation applied to 21 species (31.15%) and the oral route was most common (56.1%) while 31.2% of medicinal plants were used for both oral and topical applications. Fifty health disorders were recorded and grouped in 15 categories. Maximum species were used to treat gastrointestinal disorders i.e. 13 species, dermal problems (12 species), and respiratory tract ailments (9). The calculated RFCs ranged between 81 to 31. The most important medicinal plants were Acacia modesta, Citrullus vulgaris, Tamarindus indica, and Momordica charantia with an RGFC of 81 each. The UV ranged between 0.58 and 3.6. Medicinal taxa with the highest UV were Dioscorea deltoidea (3.6), Withania coagulans (3.3), Momordica charantia (3.5), Silybum marianum and Pyrus pashia (3.2). FL values showed that 28 (41.79%) species had a FL value below 50 (74.62%) while 39 (58.20%) had higher FL values. Momordica charantia, Tamarindus indica, Acacia modesta and Citrullus vulgaris were 95.2 each. The Jaccard Index (JI) values ranged from16.77 to 0.98. The current study also reported 16 medicinal plants, commonly used around the globe, have been rarely documented for their medicinal values in the local ethnomedicinal literature i.e. Althaea officinalis, Plantanus orientalis, Jasminum sombac, Maytenus royleana, Cucurbita maxima, Phyllanthus emblica, Citrullus vulgaris. Polygonatum verticilliatum, Caseria tomentosa, Cistanche tubulosa, Bambusa arundinacea, Schinus molle, Tamarindus indica, Pongamia pinnata, Citrus limon and Catharanthus roseus. However, 48 medicinal plants had been reported in the literature but the current study reported their novel medicinal uses. Important taxa should be established in botanical gardens for in-situ conservation, chemical investigation and sustainable utilization. It would also be effective to improve the livelihoods of the local population.

A novel approach to Cestrum intermedium (mata-boi): anatomical and physical-chemical characterization, in vitro biological activities, and metabolites of a Brazilian native species

Abstract The Brazilian native species Cestrum intermedium, known as mata-boi, induces hepatotoxicity and death when ingested by cattle. While most studies on this species focus on toxicological features, our study is the first to describe the anatomy and in vitro biological activities of Cestrum intermedium. We investigated adult leaves and stems by histochemistry, described their anatomy, performed physical-chemical analysis, determined in vitro antioxidant and antimicrobial activities, and identified secondary metabolites. A few noteworthy anatomical features were the anomocytic stomata on the abaxial surface and the absence of trichomes, in addition to the circular shaped petiole with two projections on the adaxial surface. Histochemical analysis showed chemical markers such as alkaloids, usually reported as toxic, and terpenoids. Potassium nitrate (ATR-FTIR) and lupeol palmitate (NMR) were detected on the crude stem extract. Thermogravimetric and physical-chemical analysis provided fingerprint parameters for the species. Minimal Inhibitory Concentration (MIC) assay revealed that Staphylococcus aureus, Staphylococcus epidermidis, and Candida albicans were weakly inhibited by extract samples. Chloroform and ethyl acetate fractions presented high phenolic content, which resulted in in vitro antioxidant activity. These novel features expand the knowledge about this species, considering that previous studies mainly focused on its toxicity. Our study also provided characteristics that may help in avoiding misidentification between Cestrum members, especially when taxonomic keys cannot be employed, as in the absence of flowers and fruits.

Wolfberry genomes and the evolution of Lycium (Solanaceae).

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

Withanolides from the genus Exodeconus (Solanaceae). Chemotaxonomical considerations.

Five Exodeconus species were phytochemically analyzed. From the aerial parts of E. pusillus, the 7α,27-dihydroxy-1-oxo-22R-witha-2,5,24-trienolide and three other previously unreported normal-type withanolides were isolated. All the studied species had normal type and/or ring-D aromatic withanolides, and some had already been isolated from other Solanaceae genera, and therefore, these compounds are not chemotaxonomic markers at the generic level. The chemical composition of an undescribed Exodeconus species analyzed here supports the designation of this taxon as a new entity. The integral chemical profile of Exodeconus can be evaluated for its taxonomic implication when a more robust phylogeny of Solanaceae is available that allows the phylogenetic relationships with its closest genera to be clarified.

Biogeographical, ecological, and phylogenetic analyses clarifying the evolutionary history of Calibrachoa in South American grasslands.

Calibrachoa is a charismatic South American genus of Solanaceae, closely related to Petunia, which encompasses approximately 30 species. Studies that were based solely on plastid molecular markers indicated the monophyly of the genus and distributed its species in two subgenera; to date no phylogeny has included a broad morphological variants and nuclear markers. Here, we present a phylogenetic analysis based on eight plastid and eight nuclear markers that cover the most extensive geographic distribution for the genus. We use this phylogeny to infer the biogeographic history of the genus and to understand the primary drivers for species diversification. Our results yield a fully supported tree where monophyly is confirmed to genus and subgenera. The species of Stimomphis subgenus that were previously considered uncertain, here emerge in four highly supported clades. The hypothesis of niche conservatism is confirmed, and adaptive radiation explains the species diversification. The lowlands are the most likely ancestral area of the genus, subgenera, and two clades of Stimomphis subgenus. Our results constitute an excellent starting point for further evolutionary and taxonomic studies and explain several uncertain evolutionary relationships in the group and the evolution of their distribution.

BcXyl, a ß-xylosidase Isolated from Brunfelsia Calycina Flowers with Anthocyanin-ß-glycosidase Activity.

Brunfelsia calycina flowers lose anthocyanins rapidly and are therefore well suited for the study of anthocyanin degradation mechanisms, which are unclear in planta. Here, we isolated an anthocyanin-ß-glycosidase from B. calycina petals. The MS/MS (Mass Spectrometry) peptide sequencing showed that the enzyme (72 kDa) was a ß-xylosidase (BcXyl). The enzyme showed high activity to p-Nitrophenyl-ß-d-galactopyranoside (pNPGa) and p-Nitrophenyl-ß-d-xylopyranoside (pNPX), while no activity to p-Nitrophenyl-ß-d-glucopyranoside (pNPG) or p-Nitrophenyl-ß-D-mannopyranoside (pNPM) was seen. The optimum temperature of BcXyl was 40 °C and the optimum pH was 5.0. The enzyme was strongly inhibited by 1 mM D-gluconate and Ag⁺. HPLC (High Performance Liquid Chromatography) analysis showed that BcXyl catalyzed the degradation of an anthocyanin component of B. calycina, and the release of xylose and galactose due to hydrolysis of glycosidic bonds by BcXyl was detected by GC (Gas Chromatography) /MS. A full-length mRNA sequence (2358 bp) of BcXyl (NCBI No. MK411219) was obtained and the deduced protein sequence shared conserved domains with two anthocyanin-ß-glycosidases (Bgln and BadGluc, characterized in fungi). BcXyl, Bgln and BadGluc belong to AB subfamily of Glycoside hydrolase family 3. Similar to BcPrx01, an anthocyanin-degradation-related Peroxidase (POD), BcXyl was dramatically activated at the stage at which the rapid anthocyanin degradation occurred. Taken together, we suggest that BcXyl may be the first anthocyanin-ß-glycosidase identified in higher plants.

Tandem gene duplication and recombination at the AT3 locus in the Solanaceae, a gene essential for capsaicinoid biosynthesis in Capsicum.

Capsaicinoids are compounds synthesized exclusively in the genus Capsicum and are responsible for the burning sensation experienced when consuming hot pepper fruits. To date, only one gene, AT3, a member of the BAHD family of acyltransferases, is currently known to have a measurable quantitative effect on capsaicinoid biosynthesis. Multiple AT3 paralogs exist in the Capsicum genome, but their evolutionary relationships have not been characterized well. Recessive alleles at this locus result in absence of capsaicinoids in pepper fruit. To explore the evolution of AT3 in Capsicum and the Solanaceae, we sequenced this gene from diverse Capsicum genotypes and species, along with a number of representative solanaceous taxa. Our results revealed that the coding region of AT3 is highly conserved throughout the family. Further, we uncovered a tandem duplication that predates the diversification of the Solanaceae taxa sampled in this study. This pair of tandem duplications were designated AT3-1 and AT3-2. Sequence alignments showed that the AT3-2 locus, a pseudogene, retains regions of amino acid conservation relative to AT3-1. Gene tree estimation demonstrated that AT3-1 and AT3-2 form well supported, distinct clades. In C. rhomboideum, a non-pungent basal Capsicum species, we describe a recombination event between AT3-1 and AT3-2 that modified the putative active site of AT3-1, also resulting in a frame-shift mutation in the second exon. Our data suggest that duplication of the original AT3 representative, in combination with divergence and pseudogene degeneration, may account for the patterns of sequence divergence and punctuated amino acid conservation observed in this study. Further, an early rearrangement in C. rhomboidium could account for the absence of pungency in this Capsicum species.

Scanning Electron Microscopy (SEM) and Light Microscopy (LM)-based Palyno-morphological views of Solanaceae in Western Himalaya.

In this study, plants belonging to family Solanaceae growing in Western Himalaya region have been observed palynologically under Light Microscope and Scanning electron microscope. Present investigation comprises of 10 genera and 23 species, namely, Atropa acuminata, Capsicum decoraticus, Capsicum frutescens, Cestrum aurantiacum, Cestrum diurnum, Cestrum nocturnum, Datura alba, Datura innoxia, Datura stramonium, Hyoscymus niger, Lycopersicon esculentum, Nicotiana rustica, Nicotiana tabacum, Petunia alba, Petunia hybrida, Solanum erianthum, Solanum melongena, Solanum miniatum, Solanum pseudocapsicum, Solanum surratense, Solanum tuberosum, Withania coagulans, Withania somnifera. Solanaceae is a eurypalynous family. Grains are usually Tricolporate and Tetracolporate, radially symmetrical, isopolar, prolate-spheroidal to oblate-spheroidal to oblate-spheroidal to subprolate to per prolate or suboblate to oblate, size range: 8.55-72 µm, amb circular, semi-angular or subangular, aperture drop-type, labrum common-type, exine usually 2 µm thick, nexine 1-1.5 µm thick. Tectum usually psilate, sexine reticulate, granulate or striato-reticulate, with obscure pattern, sexine 1-2 µm thick, nexine 1-1.5 µm thick, and intine 0.5-1 µm thick. Most striking variation has been found in the shape class, aperture-type, and tectal surface. Based on these characters, taxonomic keys have been made for correct identification of members in Solanaceae. However, the grains of this family are usually tricolporate and have direct relationship with certain members of the family Scrophulariaceae. Palyno-morphological characters of family Solanaceae have been studied for the first time in Western Himalayan region of Pakistan. These palyno-morphological characters are significant for identification of the members of family Solanaceae.

A new commelinid monocot seed fossil from the early Eocene previously identified as Solanaceae.

PREMISE OF THE STUDY: Fossils provide minimum age estimates for extant lineages. Here we critically evaluate Cantisolanum daturoides Reid & Chandler and two other early putative seed fossils of Solanaceae, an economically important plant family in the Asteridae. METHODS: Three earliest seed fossil taxa of Solanaceae from the London Clay Formation (Cantisolanum daturoides) and the Poole and Branksome Sand Formations (Solanum arnense Chandler and Solanispermum reniforme Chandler) were studied using x-ray microcomputed tomography (MCT) and scanning electron microscopy (SEM). KEY RESULTS: The MCT scans of Cantisolanum daturoides revealed a high level of pyrite preservation at the cellular level. Cantisolanum daturoides can be clearly excluded from Solanaceae and has more affinities to the commelinid monocots based on a straight longitudinal axis, a prominent single layer of relatively thin-walled cells in the testa, and a clearly differentiated micropyle surrounded by radially elongated and inwardly curved testal cells. While the MCT scans show no internal preservation in Solanum arnense and Solanispermum reniforme, SEM images show the presence of several characteristics that allow the placement of these taxa at the stem node of Solanaceae. CONCLUSIONS: Cantisolanum daturoides is likely a member of commelinid monocots and not Solanaceae as previously suggested. The earliest fossil record of Solanaceae is revised to consist of fruit fossil with inflated calyces from the early Eocene of Patagonia (52 Ma) and fossilized seeds from the early to mid-Eocene of Europe (48-46 Ma). The new identity for Cantisolanum daturoides does not alter a late Cretaceous minimum age for commelinids.

Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae).

Advances in sequencing technology have made it possible to produce large multi-locus datasets required for species tree analyses. One challenge with constructing high throughput sequencing datasets, however, is that missing information is propagated at different steps in the sequence preparation process. To date, species tree studies have focused on filtering and removing errors that occur at particular loci. Given the way that high throughput sequencing datasets are constructed, however, large amounts of error or ambiguity may also manifest across individuals. Here we use a novel tree-based multivariate clustering method to identify and remove individuals with low phylogenetic signal in a nuclear sequence capture dataset for the Iochrominae clade (Solanaceae). Our results suggest that the low quality tips are the result of the library preparation process (e.g. unequal pooling) rather than poor capture due to phylogenetic distance from the reference species. After implementing the clustering approach and removing low quality tips, we construct an Iochrominae species tree that resolves a number of unknown relationships. We propose this pipeline as a valuable tool for species tree reconstruction with phylogenomic datasets containing variable levels of missing data.

Phylogenetic relationships of Deprea: New insights into the evolutionary history of physaloid groups.

Deprea is the genus with the second highest species richness in tribe Physalideae (Solanaceae) and comprises 50 species that are mainly distributed in the Andes of South America. The taxonomy of Deprea has been unstable after controversial hypotheses about its position and circumscription. Additionally, biogeographical inferences are only based on observations of the restricted area of distribution of some species and no ancestral area estimation have been performed. Here, we present a phylogenetic analysis and an ancestral area reconstruction of Deprea in order to establish its circumscription, resolve its position within Physalideae, and reconstruct its biogeographical history. Phylogenetic analyses were conducted using Maximum Likelihood and Bayesian approaches. Forty-three Deprea species and 26 related taxa were sampled for three DNA markers (psbA-trnH, ITS, and waxy). A Bayesian binary MCMC model was applied in order to infer ancestral areas. Deprea is resolved as a strongly supported monophyletic group according to its current circumscription and is placed within subtribe Withaninae of Physalideae. The phylogenetic relationships enabled us to solve taxonomic problems including the rejection and acceptance of previous synonyms. The most probable ancestral area for Deprea is the Northern Andes of South America and the Amotape-Huancabamba zone. Our phylogeny provides increased resolution and support for the current position and circumscription of Deprea. Better resolution of interspecific relationships was also obtained, although some affinities remain unclear. The phylogenetic and ancestral area reconstructions provide a framework for addressing taxonomic problems and investigating new evolutionary questions.

Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway.

The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non-model plant species that remain underexplored.

Differential DNA methylation and gene expression in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.

Wide hybridization is a common and efficient breeding strategy for enhancing crop yield and quality. An interesting phenomenon is that the reciprocal hybrids usually show different phenotypes, and its underlying mechanism is not well understood. Here, we reported our comparative analysis of the DNA methylation patterns in Solanum lycopersicum, Solanum pimpinellifolium and their reciprocal hybrids by methylated DNA immunoprecipitation sequencing. The reciprocal hybrids had lower levels of DNA methylation in CpG islands and LTR retroelements when compared with those of their parents. Importantly, remarkable differences in DNA methylation patterns, mainly in introns and CDS regions, were revealed between the reciprocal hybrids. These different methylated regions were mapped to 79 genes, 14 of which were selected for analysis of gene expression levels. While there was an inverse correlation between DNA methylation and gene expression in promoter regions, the relationship was complicated in gene body regions. Further association analysis revealed that there were 15 differentially methylated genes associated with siRNAs, and that the methylation levels of these genes were inversely correlated with respective siRNAs. All these data raised the possibility that the direction of hybridization induced the divergent epigenomes leading to changes in the transcription levels of reciprocal hybrids.

Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species.

Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation. The NBS-encoding genes therefore exhibit diverse and dynamic evolutionary patterns in the three Solanaceae species, giving rise to the discrepant gene numbers observed today. Potato shows a "consistent expansion" pattern, tomato exhibits a pattern of "first expansion and then contraction," and pepper presents a "shrinking" pattern. The earlier expansion of CNLs in the common ancestor led to the dominance of this subclass in gene numbers. However, RNLs remained at low copy numbers due to their specific functions. Along the evolutionary process of NBS-encoding genes in Solanaceae, species-specific tandem duplications contributed the most to gene expansions.

Quantifying Age-dependent Extinction from Species Phylogenies.

Several ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic trees, assuming species lifetimes are gamma distributed. Testing on simulated trees shows that neglecting age dependence can lead to biased estimates of key macroevolutionary parameters. We then apply this method to two real data sets, namely a complete phylogeny of birds (class Aves) and a clade of self-compatible and -incompatible nightshades (Solanaceae), gaining initial insights into the extent to which age-dependent extinction may help explain macroevolutionary patterns. Our methods have been added to the R package TreePar.

Safety assessment and behavioral effects of Solanum guaraniticum leaf extract in rats

ABSTRACT Solanum guaraniticum is a medicinal plant traditionally used to treat gastric and liver diseases. However, there is no documented evidence corroborating its safety. The present study evaluated the potential toxicity of S. guaraniticum leaf extract after acute administration in rats. Single doses of the extract (1.250, 2.500, and 5.000 mg/kg) were administered by gavage, and the rats were then monitored for 48 h and/or 14 days. Mortality, acute signs of toxicity, and general activity in the open field test were assessed as well as hematological and biochemical parameters, enzymatic activity (δ-aminolevulinate dehydratase and acetylcholinesterase), and oxidative stress parameters (lipid peroxidation level, non-protein thiol content, tissue catalase activity, and serum ferrous reducing power). Phytochemical analysis was also performed by HPLC. The results showed that extract administration produced no deaths (LD50 > 5,000 mg/kg), and no significant adverse effects regarding food consumption, body weight gain, gross pathology, or other parameters. However, the open field tests showed a decrease in spontaneous activity (crossing and rearing) mainly at 48 h after treatment. The results suggest that S. guaraniticum extract is not acutely toxic, but causes alterations in central nervous system activity.

RESUMO Solanum guaraniticum é uma planta medicinal tradicionalmente usada para tratar doenças gástricas e hepáticas. Porém, não há evidências documentadas sobre sua segurança. O presente estudo avaliou a toxicidade do extrato das folhas de S. guaraniticum após administração aguda em ratos. Doses únicas do extrato (1.250, 2.500 and 5.000 mg/kg) foram administradas por gavagem e os animais foram monitorados por 48 h ou 14 dias. Mortalidade, sinais de toxicidade aguda e atividade geral, através do teste de campo aberto, foram analisados, assim como parâmetros hematológicos e bioquímicos, atividades enzimáticas (δ-aminolevulinato desidratase e acetilcolinesterase) e parâmetros de estresse oxidativo (nível de peroxidação lipídica, conteúdo de tióis não protéicos, atividade da catalase em tecidos e poder redutor em soro). A análise fitoquímica também foi realizada por HPLC. Os resultados mostraram que a administração do extrato não provoca mortes (LD50>5.000 mg/kg) ou efeitos adversos significativos com relação ao consumo de comida, ganho de peso corporal, análise patológica, entre outros. Entretanto, o teste de campo aberto mostrou uma diminuição na atividade espontânea geral (cruzamentos e levantadas), principalmente em 48 h após o tratamento. Portanto, nossos resultados sugerem que o extrato de S. guaraniticum não é agudamente tóxico, mas causa alterações na atividade do sistema nervoso central.

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data.

BACKGROUND: Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances. RESULTS: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on genome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% identification accuracy at supra-species level and 78% accuracy at the species level. CONCLUSION: CNIDARIA allows for fast, resource-efficient comparison and identification of both raw and assembled genome and transcriptome data. This can help answer both fundamental (e.g. in phylogeny, ecological diversity analysis) and practical questions (e.g. sequencing quality control, primer design).

Tropane alkaloids and calystegines as chemotaxonomic markers in the Solanaceae.

This study assessed the occurrence and distribution of tropane alkaloids and calystegines in genera of the family Solanaceae to identify patterns of distribution and make evolutionary inferences. A database of tropane alkaloids and calystegines occurrences was constructed from the results of a search of scientific websites and a hand search of periodicals. The terms "Solanaceae", "tropane alkaloids", and "calystegines" were used as index terms for a full-text article search unrestricted by date of publications. The number of occurrence and chemical diversity indices were calculated and cluster analysis and principal components analysis were performed. Overall, 996 occurrences were reported, 879 of tropane alkaloids (88.3%) and 117 of calystegines (11.7%). The calystegines were significantly more relevant than tropane alkaloids for characterization of distinct groups of genera on both analyses performed here. This corroborates the trend toward a chemical dichotomy observed on database analysis and somewhat reinforces the correlation between geographic distribution and occurrence of secondary metabolites, as the presence of calystegines alone (without tropane alkaloids) was only reported in genera that have South America as their center of diversity.

High genetic abundance of Rpi-blb2/Mi-1.2/Cami gene family in Solanaceae.

BACKGROUND: Three NBS-LRR genes, Rpi-blb2, Mi-1.2, and Cami, constitute a very special plant resistance gene family. These genes confer resistance against 4 distantly related pathogen species in 3 different Solanaceae hosts. To characterize this noted resistance, we conducted a series of studies on this gene family. RESULTS: First, homologs of this gene family were identified in the pepper, tomato and potato genomes. This revealed a large variation in copy number within this gene family among species and a great divergence was found both between and within species. To gain more information pertaining to gene resistance within this family, 121 LRR regions were cloned in 16 different wild/cultivated potato accessions. Again, frequent copy number variations and a high level of divergence between homolog were observed common among accessions. The divergence within species was so high that it reaches the level of divergence between species. Also, frequent frameshift mutations and abundant gene conversion events were identified in these LRR regions. CONCLUSIONS: Our findings suggest that this family harbors an unusually high level of genetic abundance, making it of particular interest. Together with other reported examples, our study also provides evidence that multi-resistance is a common trait in R gene families like this.