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Coffea canephora, (Robusta), provides 33% of worldwide coffee production, 80% and 22% of Ugandan and Brazilian coffee production, respectively. Abiotic stress such as temperature variations or drought periods, aggravated by climate... more
Coffea canephora, (Robusta), provides 33% of worldwide coffee production, 80% and 22% of Ugandan and Brazilian coffee production, respectively. Abiotic stress such as temperature variations or drought periods, aggravated by climate changes, are factors that affect this production. This sensitivity threatens both the steady supply of quality coffees and the livelihood of millions of people producing coffee. The natural genetic diversity of C. canephora offer a potential for detecting new genetic variants related to drought adaptation. In particular, modifications occurring in genes related to abiotic stress tolerance make these genes candidate for breeding programs in order to enhance the resilience to climate change.
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Rice tungro disease is caused by rice tungro bacilliform virus (RTBV), which is responsible for the symptoms, and rice tungro spherical virus (RTSV), which assists transmission of both viruses by leafhoppers. Transgenic japonica rice... more
Rice tungro disease is caused by rice tungro bacilliform virus (RTBV), which is responsible for the symptoms, and rice tungro spherical virus (RTSV), which assists transmission of both viruses by leafhoppers. Transgenic japonica rice plants (Oryza sativa) were produced containing the RTSV replicase (Rep) gene in the sense or antisense orientation. Over 70% of the plants contained one to five copies of the Rep gene, with integration occurring at a single locus in most cases. Plants producing antisense sequences exhibited significant but moderate resistance to RTSV (60%); accumulation of antisense RNA was substantial, indicating that the protection was not of the homology-dependent type. Plants expressing the full-length Rep gene, as well as a truncated Rep gene, in the (+)-sense orientation were 100% resistant to RTSV even when challenged with a high level of inoculum. Accumulation of viral RNA was low, leading us to conclude that RTSV Rep-mediated resistance is not protein-mediated ...
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Research Interests: Genetics, Genomics, Computational Biology, Comparative Genomics, Biology, and 15 moreFunctional Genomics, Genetic Diversity, Expressed Sequence Tags, DNA sequence design, Genome, Computer User Interface Design, Fruit set and development, Association Mapping, Genome sequence, Coffea arabica, Database, Coffea, DNA sequence, Fruit Development, and Functional Annotation
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A set of 867 COSII markers allowed to established macrosynteny between coffee, tomato and grapevine. Coffee and tomato genomes shared 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine shared a similar... more
A set of 867 COSII markers allowed to established macrosynteny between coffee, tomato and grapevine. Coffee and tomato genomes shared 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine shared a similar number of syntenic markers (299) and CSSs (29). Despite important genome macrostructure reorganization, several large chromosome segments showed exceptional macrosynteny, shedding new insights into chromosome evolution between flowering plants. In addition, we analyzed a BAC sequence of 174 kb containing the Ovate gene, conserved in a syntenic block between the three plants, that showed a high microsynteny conservation. Surprisingly, a higher level of conservation was observed between coffee and grapevine, both ligneous and perennial plants, than between coffee and tomato, an annual plant. Out of 16 genes identified in coffee on this segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. A significant conservation was found at the macro- and micro-structure levels between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades. Conservation did not decline at the Ovate locus in relation to phylogenetic distance, suggesting that the time factor alone does not explain all the divergences. These results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy. (Resume d'auteur)
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Chlorogenic acids (CGA) are products of phenylpropanoid metabolism, i.e. one branch of the phenolic pathway. A wild species, Coffea pseudozanguebariae, native of East Africa, is a caffeine-free species with low CGA content (1.2% dmb in... more
Chlorogenic acids (CGA) are products of phenylpropanoid metabolism, i.e. one branch of the phenolic pathway. A wild species, Coffea pseudozanguebariae, native of East Africa, is a caffeine-free species with low CGA content (1.2% dmb in green beans). It is also used as a gene donor to improve C. canephora cup taste quality. In the current study, contents of the different CGA isomers were observed during the development in fruits and leaves. In both organs, CGA content decreased strongly during the growth and feruloylquinic acids (FQA) constituted most CGA. In fruits, a critical step was emphasised at the growth end, beyond which caffeoylquinic acid content (CQA) drastically increased. Previous results on beans suggest that the qualitative change concerned seeds and not pulp. The breeding implications and potential for further studies are discussed.
Research Interests: Horticulture and Biology
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Research Interests: Genetics, Coffee, Biology, Medicine, FISH, and 7 moreGenome, Gypsy, Coffea arabica, Centromeres, Ploidy, centromere, and Coffea Canephora
Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing... more
Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long‐lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy‐one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB‐like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate‐associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.
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RATIONALE Testing whether and how natural populations are adapted to their local environment and predicting their response to future habitat alterations is of key importance in the face of future climate change. This is particulary the... more
RATIONALE Testing whether and how natural populations are adapted to their local environment and predicting their response to future habitat alterations is of key importance in the face of future climate change. This is particulary the case for coffee trees for which the pace of climate change could be too fast and drastic for population adaptations. Using the geographic distribution of wild populations with contrasted habitats, the aim of the present study was to identify single-nucleotide polymorphisms (SNPs) in candidate genes (CGs) identified as being involved in the adaptation of C. canephora populations to their local environment. By identifying environmental factors driving these processes we would predict the adaptedness of the populations to their future local climate. METHODS Based on the previous molecular studies (EMBRAPA/CIRAD/Nestle studies) and using whole coffee genome sequence annotation (Denoeud et al. 2014, Dereeper et al. 2015), a set of 324 CGs was selected, such as those coding for dehydrins, heat shock proteins, enzymes of sugar metabolism, as well as transcription factors like DREB/CBF (dehydration responsive element binding/cold-binding factor). Wild accessions of C. canephora from Uganda with recorded position (geo-localized samples) were used to assess the relationship between climate variation (www.worldclim.org/bioclirn) and CG nucleic diversity. We apply available statistical population genomic methods and model of allele distribution to detect CGSNPs correlated with climate parameters. The LFMM (Latent Factor Mixed Models) R package (Frichot et al. 2013) was used for screening sequences for signatures of environmental adaptation in coffee genomes. RESULTS The genotype-environment (GxE) association suggests regional adaptation with spatially varying environments. More specifically, we found selection signals tightly linked to several CGs involved in response to biotic and abiotic stress like MYB20 (coding a transcription factor involved in the response to drought stress) and DXMT (enzyme involved in caffeine biosynthesis) genes. CONCLUSIONS &PERSPECTIVES The selection signals detected support the hypothesis of present ecological gradient contributing to structure of the genetic diversity of U gandense C. canephora populations. The amount and character of genetic variations observed in genomic regions associated with climatic variables will help us to predict whether C. canephora species will be able to adapt quickly enough to track global warming.
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The ability of crops to adapt to environmental changes such as the predicted climate change strongly depends on the genetic variation that exists within the crops.
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An international consortium was initiated in 2012 with the goal to perform the sequencing of the Coffea arabica genome. This consortium includes 34 researchers, engineers and technicians coming from 13 institutions in six different... more
An international consortium was initiated in 2012 with the goal to perform the sequencing of the Coffea arabica genome. This consortium includes 34 researchers, engineers and technicians coming from 13 institutions in six different countries. In December 2013 the first draft genome of a Coffea species was published in Science (Denoeud et al. 2014), it is the genome of the C. canephora species, a diploid and the second mainly cultivated species after C. arabica. This later species is the only tetraploid of the genus resulting from a recent spontaneous hybridization (± 0,5 Mya) between C. eugenioides, a wild species from East Africa, and C. canephora, whose genome was sequenced (Lashermes et al. 1999).
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Research Interests: Chemistry, Analytical Chemistry, Electrochemistry, Catalysis, Kinetics, and 12 moreAmylose, Enzyme, High Pressure Liquid Chromatography, Molecular Mass, Mechanism of action, Hydrolysis, Amylase, Biochemistry and cell biology, Oligosaccharides, Lactobacillus fermentum, Maltose, and Pharmacology and pharmaceutical sciences
ABSTRACT The genus Coffea, mainly native to Africa and to the Indian Ocean islands (Mascarocoffea), accounts for 124 species. Genome size data are available for 23 African species. The aim of this study was to assess the genome size of 44... more
ABSTRACT The genus Coffea, mainly native to Africa and to the Indian Ocean islands (Mascarocoffea), accounts for 124 species. Genome size data are available for 23 African species. The aim of this study was to assess the genome size of 44 Mascarocoffea species and to investigate possible association with species geographic distribution, stomata traits, and species relationships. 2 C values were measured using flow cytometry. A lyophilization procedure for leaves was tested. The 2 C nuclear DNA content of Mascarocoffea species ranged from 0.96 to 1.41 pg. Coffea mauritiana and Coffea humblotiana have the smallest genomes and Coffea millotii has the largest. Mean 2 C DNA for Mascarocoffea and Africa is 1.19 and 1.43 pg, respectively. The overall DNA values corresponded to two partially overlapped normal distributions: one harboring species from east Africa Mascarocoffea, the other harboring species from west/central Africa. Plotted on a geographical map according to the native origin of species, these values showed a gradient in Madagascar and Africa. Genome sizes increased following a north to southeast gradient in Madagascar and an east to west gradient in Africa. None, or only weak correlations were noted between genome size and stomata parameters. Genetically close species could be highly distinctive in their genome size while divergent species could be similarly sized. The non-random geographic distribution and habitat of species, and the absence of correlation between genome size and genetic relationships, suggest that during Coffea genome evolution, both DNA content increase and/or decrease occurred independently in Africa and in the Indian Ocean Islands.
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The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the... more
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species’ native range can provide valuable insights about habitat loss and the species’ adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vul...
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Like many other crops, coffee production is threatened by climate changes. Therefore, research on coffee adaptation to abiotic stresses as well as alternative faster breeding programs are priorities in many coffee growing countries.... more
Like many other crops, coffee production is threatened by climate changes. Therefore, research on coffee adaptation to abiotic stresses as well as alternative faster breeding programs are priorities in many coffee growing countries. During the last decade, studies have been focused on identifying the physiological, molecular and genetic determinisms of coffee drought‐tolerance, mainly on C. canephora. By comparing drought‐tolerant and ‐susceptible clones, several candidate genes (like CcDREB1D) were highlighted. Recent studies demonstrated that CcDREB1D promoter haplotypes differentially regulate the expression of this gene under drought (and other abiotic stresses), mainly in leaf guard cells. In order to predict the adaptedness of C. canephora populations to climate change, statistical analyses are in progress to associate SNPs found in such candidate genes with climate parameters. Regarding C. arabica, new F1 hybrids resulting from conventional varieties crossed with wild Ethiopi...
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Coffee is the most traded crop by Southern countries and is the main source of income for more than 75 millions small farmers all over the world. Despite its economical importance and the obvious necessity to improve the crop in order to... more
Coffee is the most traded crop by Southern countries and is the main source of income for more than 75 millions small farmers all over the world. Despite its economical importance and the obvious necessity to improve the crop in order to respond to new environmental constraints and to the consumer demand for quality, the sequencing of its genome only started in late 2009. An international consortium was formed, led by Genoscope, to perform this task. Coffea canephora, a diploid cultivated species, was chosen, since C. arabica is tetraploid. Furthermore, IRD developed a double haploid plant because C. canephora is allogamous. Its genome size is about 695 Mb and whole genome sequencing is being performed using NGS complemented by BAC ends coming from two BAC libraries covering in total 14.8 genome equivalents. SSR markers mined from these sequences are being mapped to establish a consensus genetic map based on the map kindly provided by Nestle and ICCRI. Both Roche pyrosequencing (454...
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Commercial coffee production relies mainly on two closely related species: Coffea arabica and C. canephora, which account respectively for 70 and 30% of the coffee production. All coffee species are diploid (2n=2x=22) and generally... more
Commercial coffee production relies mainly on two closely related species: Coffea arabica and C. canephora, which account respectively for 70 and 30% of the coffee production. All coffee species are diploid (2n=2x=22) and generally selfincompatible, except for C. arabica which is the only tetraploid (2n=4x=44) and self-fertile. Molecular analyses (Lashermes et al. 1999) have indicated that C. arabica is a recent allotetraploid (CE genome) formed by hybridisation between two related diploid species: C. canephora (C genome) and C. eugenioides (E genome). In spite of the close relationship between the two constitutive sub-genomes, C. arabica displays diploid-like meiotic behavior with bivalent formation (Krug and Mendes 1940, Lashermes et al. 2000). The genomes of coffee species (Cros et al. 1995; Noirot et al. 2003) appear to be of rather low size (i. e. about 660, 710 and 1300 Mb for C. eugenioides, C. canephora and C. arabica, respectively). Several institutes are combining their sc...
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Research Interests: Geology, Image Processing, Remote Sensing, Neural Networks, New Caledonia, and 15 moreNeural Network, Canopy, Geomatic Engineering, Decision Tree, Introduced species, Digital Elevation Model, Forest Classification, Coffea arabica, Complex Structure, Environmental Parameter, High Resolution Satellite Imagery, Coffea, Multispectral image, Confidence Level, and Canopy cover
A library enriched in repeated sequences was obtained from a F1 hybrid issued from a cross between C pseudozanguebariae and C. liberica var. dewevrei. These two species differ in their nuclear DNA content, 1.3 pg and 1.43 pg... more
A library enriched in repeated sequences was obtained from a F1 hybrid issued from a cross between C pseudozanguebariae and C. liberica var. dewevrei. These two species differ in their nuclear DNA content, 1.3 pg and 1.43 pg respectivelly. 193 clones were isolated following retrohybridization. Already 60 clones have been sequenced and show a great proportion of repeated sequences (>90%). In addition to tandemly repeated sequences, several types of retrotransposons have been identified following similitude comparison (BLAST) with data bases. Both types gypsy-like and copia-like are present in Coffea genomes. Furthermore, other LINE retrotransposons were also detected. Probes corresponding to some of these repeated sequences were hybridized to nuclear DNA isolated from several Coffea species: C rasemosa, C. sessiflora, C. eugenioides, C. sp. Moloundou, C. canephora, C. congensis and C. heterocalyx. All the species contained sequencies similar to the used probes but the restriction pattern were different and identical phylogenetic groups to those determined by ribosomal DNA could be identified. Importance of repeated sequences in speciation of Coffea genus and their role in F1 sterility will be discussed. (Texte integral)
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Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing... more
Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long‐lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy‐one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB‐like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate‐associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.
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ERFs (Ethylene-Responsive Element Binding Factors) are members of a transcription factors family unique to plants. They contain a well-conserved segment, which interacts specifically with sequences containing AGCCGCC motifs (GCC box)... more
ERFs (Ethylene-Responsive Element Binding Factors) are members of a transcription factors family unique to plants. They contain a well-conserved segment, which interacts specifically with sequences containing AGCCGCC motifs (GCC box) located in the promoter region of genes activated during biotic or environmental stress in plants. A cDNA corresponding to an ERF gene has been isolated from a Coffea canephora fruit cDNA library. The cDNA was 1,317 nucleotides long and has an open reading frame of 987 bp. The predicted polypeptide showed a great similitude with equivalent proteins from others plant species. The binding domain shows 98.3% identity in amino acids sequence with Lycopersicon esculentum ERF. This transcription factor may possibly be involved in differential cell growth or in fruit ripening process. Although it was not possible to isolate it from a leaf cDNA library, its presence in such library was confirmed. African Journal of Biotechnology Vol. 4 (2), pp. 157-159, 2005
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Centromeric regions of plants are generally composed of large array of satellites from a specific lineage ofLTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a... more
Centromeric regions of plants are generally composed of large array of satellites from a specific lineage ofLTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in the genus, we annotated and classified Centromeric Retrotransposons sequences from the allotetraploidgenome and its two diploid ancestors:and. Ten distinct CRC (Centromeric Retrotransposons in) families were found. The sequence mapping and FISH experiments of CRC Reverse Transcriptase domains in, andclearly indicate a strong and specific targeting mainly onto proximal chromosome regions, which can be associated also with heterochromatin. PacBio genome sequence analyses of putative centromeric regions onandchromosomes showed an exceptional density of one family of CRC elements, and the complete absence of satellite arrays, contrasting with usual str...
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Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration... more
Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population h...
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Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation... more
Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains. Reverse Trancriptase (RT) domain-based phylogeny demonstrated that Divo is a new and well-supported family in the Bianca lineage, but strictly restricted to dicotyledonous species. In C. canephora, Divo is expressed and showed a genomic distribution along gene rich and gene poor regions. The copy number, the molecular estimation of insertion time and the analysis at orthologou...
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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... more
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.