Publications by authors named "Piet Stoffelen"

15 Publications

  • Page 1 of 1

Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation.

Am J Bot 2021 Oct 11. Epub 2021 Oct 11.

Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.

Premise: Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo.

Methods: Using 18 microsatellite markers, we studied the genetic composition of wild and backyard-grown C. canephora shrubs in the Tshopo and Ituri provinces, and from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations.

Key Results: Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi.

Conclusions: Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes, to increase the genetic resources available for breeding purposes, as well as to support ex situ conservation. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1002/ajb2.1769DOI Listing
October 2021

Coffee Leaves: An Upcoming Novel Food?

Planta Med 2021 Oct 24;87(12-13):949-963. Epub 2021 Sep 24.

RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium.

Unlike those of coffee beans, the healthy properties of coffee leaves have been overlooked for a long time, even if they are consumed as a beverage by local communities of several African countries. Due to the presence of xanthines, diterpenes, xanthones, and several other polyphenol derivatives as main secondary metabolites, coffee leaves might be useful to prevent many daily disorders. At the same time, as for all bioactive molecules, careless use of coffee leaf infusions may be unsafe due to their adverse effects, such as the excessive stimulant effects on the central nervous system or their interactions with other concomitantly administered drugs. Moreover, the presence of some toxic diterpene derivatives requires careful analytical controls on manufactured products made with coffee leaves. Accordingly, knowledge about the properties of coffee leaves needs to be increased to know if they might be considered a good source for producing new supplements. The purpose of the present review is to highlight the biosynthesis, metabolism, and distribution of the 4 main classes of secondary metabolites present in coffee leaves, their main pharmacological and toxicological aspects, and their main roles . Differences in coffee leaf chemical composition depending on the coffee species will also be carefully considered.
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http://dx.doi.org/10.1055/a-1533-0021DOI Listing
October 2021

When xylarium and herbarium meet: linking Tervuren xylarium wood samples with their herbarium specimens at Meise Botanic Garden.

Biodivers Data J 2021 31;9:e62329. Epub 2021 Mar 31.

Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium.

Background: The current data paper aims to interlink the African plant collections of the Meise Botanic Garden Herbarium (BR) and the Royal Museum for Central Africa Xylarium (Tw). Complementing both collections strengthens the reference value of each institutional collection, as more complete metadata are made available and it enables increased quality control for the identification of wood specimens. Furthermore, the renewed connection enables the linking of available wood trait data with data on phenology, leaf morphology or even molecular information for many tree species, allowing assessments of performance of individual trees. In addition to studies at the interspecific level, comparisons at the intraspecific level become possible, which could lead to important new insights into resilience to and impact of global change, as well as biodiversity conservation or forest management of Central African forest ecosystems.

New Information: By interlinking the Tervuren Xylarium Wood database with the recently digitised herbarium of Meise Botanic Garden, we were able to establish a link between 6,621 xylarium and 9,641 herbarium records for 6,953 plant specimens. Both institutional databases were complemented with reliable specimen metadata. The Tervuren xylarium now profits from taxonomic revisions made by botanists at Meise Botanic Garden and a list of phenotypical features for woody African species can be extended with wood anatomical descriptors. New metadata from the Tw xylarium records were used to add the country of collection to 50 linked BR herbarium specimens for which this information was missing. Furthermore, metadata available from the labels on digitised BR herbarium specimens was used to update Tw xylarium records with the date of collection (817 records), collection locality (698 records), coordinates (482 records) and altitude (817 records). In conclusion, we created a reference database with reliable botanic identities which can be used in a range of studies, such as modelling analyses, community assessments or trait analyses, all framed in a spatiotemporal context. Furthermore, the linked collections hold historical reference data and specimens that can be studied in the context of global changes.
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http://dx.doi.org/10.3897/BDJ.9.e62329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026533PMC
March 2021

Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation.

PLoS One 2021 8;16(2):e0245965. Epub 2021 Feb 8.

IRD-UMR DIADE (Univ. Montpellier, CIRAD, IRD), Montpellier, France.

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species' global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda's native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245965PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7870046PMC
July 2021

Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee).

Mol Phylogenet Evol 2020 10 10;151:106906. Epub 2020 Jul 10.

Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France; Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia. Electronic address:

For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid full-genome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
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http://dx.doi.org/10.1016/j.ympev.2020.106906DOI Listing
October 2020

Century-long apparent decrease in intrinsic water-use efficiency with no evidence of progressive nutrient limitation in African tropical forests.

Glob Chang Biol 2020 08 29;26(8):4449-4461. Epub 2020 May 29.

Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.

Forests exhibit leaf- and ecosystem-level responses to environmental changes. Specifically, rising carbon dioxide (CO ) levels over the past century are expected to have increased the intrinsic water-use efficiency (iWUE) of tropical trees while the ecosystem is gradually pushed into progressive nutrient limitation. Due to the long-term character of these changes, however, observational datasets to validate both paradigms are limited in space and time. In this study, we used a unique herbarium record to go back nearly a century and show that despite the rise in CO concentrations, iWUE has decreased in central African tropical trees in the Congo Basin. Although we find evidence that points to leaf-level adaptation to increasing CO -that is, increasing photosynthesis-related nutrients and decreasing maximum stomatal conductance, a decrease in leaf δ C clearly indicates a decreasing iWUE over time. Additionally, the stoichiometric carbon to nitrogen and nitrogen to phosphorus ratios in the leaves show no sign of progressive nutrient limitation as they have remained constant since 1938, which suggests that nutrients have not increasingly limited productivity in this biome. Altogether, the data suggest that other environmental factors, such as increasing temperature, might have negatively affected net photosynthesis and consequently downregulated the iWUE. Results from this study reveal that the second largest tropical forest on Earth has responded differently to recent environmental changes than expected, highlighting the need for further on-ground monitoring in the Congo Basin.
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http://dx.doi.org/10.1111/gcb.15145DOI Listing
August 2020

Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: The case of genus Benn.

Ecol Evol 2019 Dec 12;9(23):13114-13126. Epub 2019 Nov 12.

Evolutionary Biology and Ecology Unit Faculté des Sciences Université Libre de Bruxelles Brussels Belgium.

Adaptive evolution is a major driver of organism diversification, but the links between phenotypic traits and environmental niche remain little documented in tropical trees. Moreover, trait-niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (a) convergent evolution if different environmental conditions have selected different sets of traits, and/or (b) phylogenetic inertia if niche and morphological differences between species are simply function of their phylogenetic divergence, in which case the trait-niche correlation does not imply any direct causal link. Here, we aim to assess the respective roles of phylogenetic inertia and convergent evolution in shaping the differences of botanical traits and environmental niches among congeneric African tree species that evolved in different biomes.This issue was addressed with the tree genus Benn. (Leguminosae and Detarioideae), which contains 13 African species occupying various forest habitat types, from rain forest to dry woodlands, with different climate and soil conditions. To this end, we combined morphological data with ecological niche modelling and used a highly resolved plastid phylogeny of the 13 African species.First, we demonstrated phylogenetic signals in both morphological traits (Mantel test between phylogenetic and morphological distances between species:  = .24,  = .031) and environmental niches (Mantel test between phylogenetic and niche distances between species:  = .23,  = .025). Second, we found a significant correlation between morphology and niche, at least between some of their respective dimensions (Mantel's  = .32,  = .013), even after accounting for phylogenetic inertia (Phylogenetic Independent Contrast:  = .69,  = .018). This correlation occurred between some leaflet and flower traits and solar radiation, relative humidity, precipitations, and temperature range.Our results demonstrate the convergent evolution of some morphological traits in response to climatic factors in congeneric tree species and highlight the action of selective forces, along with neutral ones, in shaping the divergence between congeneric tropical plants.
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http://dx.doi.org/10.1002/ece3.5740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6912925PMC
December 2019

Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.

Plant Biotechnol J 2019 07 4;17(7):1418-1430. Epub 2019 Feb 4.

IRD, UMR DIADE, Montpellier, France.

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
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http://dx.doi.org/10.1111/pbi.13066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6576098PMC
July 2019

Determination of Three Main Chlorogenic Acids in Water Extracts of Coffee Leaves by Liquid Chromatography Coupled to an Electrochemical Detector.

Antioxidants (Basel) 2018 Oct 15;7(10). Epub 2018 Oct 15.

Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.

Coffee is a beverage widely consumed in the world. The coffee species most commercialized worldwide are Arabica ( and Robusta (. Roasted coffee beans are the most used, but coffee leaves are also consumed as infusion in several countries for traditional medicinal purposes. They contain several interesting phenolic antioxidant compounds mainly belonging to chlorogenic acids (CGAs). In the present work, a liquid chromatography-electrochemical detection (LC-EC) method was developed for the determination of three main chlorogenic acid isomers, namely 3-, 4-, and 5-caffeoylquinic acids (CQA), in coffee leaves aqueous extracts. Samples from eight coffee species, namely; , , , , , , , and , were grown and collected in tropical greenhouses. Linearity of the calibration graphs was observed in the range from the limit of quantification to 1.0 × 10 M, with R² equal to 99.9% in all cases. High sensitivity was achieved with a limit of detection of 1.0 × 10 M for 3-CQA and 5-CQA (i.e., 3.5 µg/L) and 2.0 × 10 M for 4-CQA (i.e., 7.1 µg/L). The chromatographic profile of the samples harvested for each species was studied comparatively. Obtained raw data were pretreated for baseline variations and shifts in retention times between the chromatographic profiles. Principal Component Analysis (PCA) was applied to the pretreated data. According to the results, three clusters of species were found. In the water sample extracts, 5-CQA appeared to be the major isomer, and some species contained a very low amount of CQAs. Fluctuations were observed depending on the species and harvesting period. Significant differences between January and July were noticed regarding CQAs content. The species with the best CQAs/caffeine ratio was identified. The LC-EC data were validated by liquid chromatography-high resolution mass spectrometry (LC-HRMS).
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http://dx.doi.org/10.3390/antiox7100143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209918PMC
October 2018

Metabolomics fingerprint of coffee species determined by untargeted-profiling study using LC-HRMS.

Food Chem 2018 Apr 12;245:603-612. Epub 2017 Oct 12.

Laboratoire de Pharmacognosie, de Bromatologie et de Nutrition Humaine, Faculté de Pharmacie, Université Libre de Bruxelles, Campus Plaine, CP 205/09, 1050 Brussels, Belgium.

Coffee bean extracts are consumed all over the world as beverage and there is a growing interest in coffee leaf extracts as food supplements. The wild diversity in Coffea (Rubiaceae) genus is large and could offer new opportunities and challenges. In the present work, a metabolomics approach was implemented to examine leaf chemical composition of 9 Coffea species grown in the same environmental conditions. Leaves were analyzed by LC-HRMS and a comprehensive statistical workflow was designed. It served for univariate hypothesis testing and multivariate modeling by PCA and partial PLS-DA on the Workflow4Metabolomics infrastructure. The first two axes of PCA and PLS-DA describes more than 40% of variances with good values of explained variances. This strategy permitted to investigate the metabolomics data and their relation with botanic and genetic informations. Finally, the identification of several key metabolites for the discrimination between species was further characterized.
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http://dx.doi.org/10.1016/j.foodchem.2017.10.022DOI Listing
April 2018

Identification of coffee leaves using FT-NIR spectroscopy and SIMCA.

Talanta 2018 Jan 23;177:4-11. Epub 2017 Sep 23.

Laboratory of Instrumental Analysis and Bioelectrochemistry, Faculty of Pharmacy, Université Libre de Bruxelles, Boulevard du Triomphe, Campus Plaine, CP 205/06, 1050, Brussels, Belgium.

Abundant literature has been devoted to coffee beans (green or roasted) chemical description but relatively few studies have been devoted to coffee leaves. Given the fact that coffee leaves are used for food and medicinal consumption, it was of interest to develop a rapid screening method in order to identify coffee leaves taxa. Investigation by Fourier - Transform near infrared spectroscopy (FT-NIRS) was performed on nine Coffea taxa leaves harvested over one year in a tropical greenhouse of the Botanic Garden Meise (Belgium). The only process after leaves harvesting was an effective drying and a homogeneous leaves grinding. FT-NIRS with SIMCA analysis allowed to discriminate the spectral profiles across taxon, aging stage (mature and senescence coffee leaves) and harvest period. This study showed that it was possible (i) to classify the different taxa, (ii) to identify their aging stage and (iii) to identify the harvest period for the mature stage with a correct classification rate of 99%, 100% and 90%, respectively.
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http://dx.doi.org/10.1016/j.talanta.2017.09.056DOI Listing
January 2018

Scientific user requirements for a herbarium data portal.

PhytoKeys 2017 24(78):37-57. Epub 2017 Mar 24.

Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium.

The digitization of herbaria and their online access will greatly facilitate access to plant collections around the world. This will improve the efficiency of taxonomy and help reduce inequalities between scientists. The Botanic Garden Meise, Belgium, is currently digitizing 1.2 million specimens including label data. In this paper we describe the user requirements analysis conducted for a new herbarium web portal. The aim was to identify the required functionality, but also to assist in the prioritization of software development and data acquisition. The Garden conducted the analysis in cooperation with Clockwork, the digital engagement agency of Ordina. Using a series of interactive interviews, potential users were consulted from universities, research institutions, science-policy initiatives and the Botanic Garden Meise. Although digital herbarium data have many potential stakeholders, we focused on the needs of taxonomists, ecologists and historians, who are currently the primary users of the Meise herbarium data portal. The three categories of user have similar needs, all wanted as much specimen data as possible, and for those data, to be interlinked with other digital resources within and outside the Garden. Many users wanted an interactive system that they could comment on, or correct online, particularly if such corrections and annotations could be used to rank the reliability of data. Many requirements depend on the quality of the digitized data associated with each specimen. The essential data fields are the taxonomic name; geographic location; country; collection date; collector name and collection number. Also all researchers valued linkage between biodiversity literature and specimens. Nevertheless, to verify digitized data the researchers still want access to high quality images, even if fully transcribed label information is provided. The only major point of disagreement is the level of access users should have and what they should be allowed to do with the data and images. Not all of the user requirements are feasible given the current technical and regulatory landscape, however, the potential of these suggestions is discussed. Currently, there is no off-the-shelf solution to satisfy all these user requirements, but the intention of this paper is to guide other herbaria who are prioritising their investment in digitization and online web functionality.
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http://dx.doi.org/10.3897/phytokeys.78.10936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543274PMC
March 2017

Exploring the floristic diversity of tropical Africa.

BMC Biol 2017 03 7;15(1):15. Epub 2017 Mar 7.

AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France.

Background: Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa.

Results: The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic.

Conclusions: The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.
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http://dx.doi.org/10.1186/s12915-017-0356-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339970PMC
March 2017

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

Mol Phylogenet Evol 2017 04 16;109:351-361. Epub 2017 Feb 16.

UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France. Electronic address:

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
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http://dx.doi.org/10.1016/j.ympev.2017.02.009DOI Listing
April 2017

RAINBIO: a mega-database of tropical African vascular plants distributions.

PhytoKeys 2016 7(74):1-18. Epub 2016 Nov 7.

Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK.

The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.
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http://dx.doi.org/10.3897/phytokeys.74.9723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234546PMC
November 2016
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