Furanocoumarins (FCs) are plant-specialized metabolites with potent allelochemical properties. The distribution of FCs is scattered with a chemotaxonomical tendency towards four distant families with highly similar FC pathways. The mechanism by which this pathway emerged and spread in plants has not been elucidated. Furanocoumarin biosynthesis was investigated in Ficus carica (fig, Moraceae), focusing on the first committed reaction catalysed by an umbelliferone dimethylallyltransferase (UDT). Comparative RNA-seq analysis among latexes of different fig organs led to the identification of a UDT. The phylogenetic relationship of this UDT to previously reported Apiaceae UDTs was evaluated. The expression pattern of F. carica prenyltransferase 1 (FcPT1) was related to the FC contents in different latexes. Enzymatic characterization demonstrated that one of the main functions of FcPT1 is UDT activity. Phylogenetic analysis suggested that FcPT1 and Apiaceae UDTs are derived from distinct ancestors, although they both belong to the UbiA superfamily. These findings are supported by significant differences in the related gene structures. This report describes the identification of FcPT1 involved in FC biosynthesis in fig and provides new insights into multiple origins of the FC pathway and, more broadly, into the adaptation of plants to their environments.

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Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam ( Dioscorea ) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy ( Dioscorea alata , D. communis , and D. sylvatica ). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea . We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.

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Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea , an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea , assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. Results The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. Discussion Our customized panel reliably retrieves targeted loci from Dioscorea , is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

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Background Wild vegetables in the Mediterranean Basin are still often consumed as a part of the diet and, in particular, there is a great tradition regarding their use in Sicily. In this study, an ethnobotanical field investigation was carried out to (a) identify the wild native taxa traditionally gathered and consumed as vegetables in Sicily, comparing the collected ethnobotanical data with those of other countries that have nominated the Mediterranean diet for inclusion in the UNESCO Representative List of the Intangible Cultural Heritage of Humanity and (b) highlight new culinary uses of these plants. Methods Interviews were carried out in 187 towns and villages in Sicily between 2005 and 2015. A total of 980 people over the age of 50 were interviewed (mainly farmers, shepherds, and experts on local traditions). Plants recorded were usually collected in collaboration with the informants to confirm the correct identification of the plants. The frequencies of citation were calculated. Results Two hundred fifty-three taxa (specific and intraspecific) belonging to 39 families, and 128 genera were recorded (26 were cited for the first time). The most represented families were Asteraceae, Brassicaceae, Apiaceae, Amaryllidaceae, Malvaceae, and Polygonaceae. Only 14 taxa were cited by 75% of the people interviewed. The aerial parts of wild plants, including leaves, tender shoots, and basal rosettes, are the main portions collected, while the subterranean parts are used to a lesser extent. For some vegetables, more parts are utilized. Most of the reported vegetables are consumed cooked. In addition to the widely known vegetables (Borago officinalis, Beta spp., Cichorium spp., Brassica spp., Carduus spp., etc.), the so-called ancient vegetables are included (Onopordum illyricum, Centaurea calcitrapa, Nasturtium officinale, Scolymus spp., Smyrnium rotundifolium), and some unique uses were described. Comparing the Sicilian findings to those from other countries, a very high number of vegetable taxa were detected, 72 of which are eaten only in Sicily, while 12 are consumed in all the Mediterranean countries examined. Conclusions The research shows a high level of Sicilian knowledge about using wild plants as a traditional food source. Wild vegetables are healthy and authentic ingredients for local and ancient recipes, which are fundamental to the revitalization of quality food strictly connected to traditional agroecosystems.

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Background Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species- ideally, as a global standard. Research question What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset. Methodology In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples. Principal findings Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names. Conclusions/significance Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range.

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