Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred similar to 30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

AbstractCoffea arabica, an allotetraploid hybrid ofC. eugenioidesandC. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploidC. arabicaaccession and modern representatives of its diploid progenitors,C. eugenioidesandC. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ∼30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed withC. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding ofC. arabica.

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N -methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome ( C. canephora ) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

This the data table of the WCSdb: A database of Wild Coffea Species web site. The photo Gallery associated to this web site are available at https://doi.org/10.23708/JZA8I2 and the sequencing data at https://doi.org/10.23708/KWRIJJ Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species belong to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by Pl@ntNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 140 coffee species, for which 84 contain a photo gallery and 82 contain sequencing data (GBS, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity, sequence data) in order to better protect and promote them.

Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species/taxa belonging to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by Pl@ntNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 141 coffee species/taxa, for which 84 contain a photo gallery and 82 contain sequencing data (genotyping-by-sequencing, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity and sequence data) in order to better protect and promote them.DATABASE URL:http://publish.plantnet-project.org/project/wildcofdb_en.

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.

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 orthologous locations of insertions in diploid and allotetraploid coffee genomes suggest that Divo underwent a different and recent transposition activity in C. arabica and C. canephora when compared to C. eugenioides . The analysis of this novel LTR-RT family represents an important step toward uncovering the genome structure and evolution of C. arabica allotetraploid genome.

The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.

Coffea arabica which accounts for 70% of world coffee production is an allotetraploid with a genome size of approximately 1.3 Gb and is derived from the hybridization of C. canephora (710 Mb) and C. eugenioides (670 Mb). To elucidate the evolutionary history of C. arabica, and generate critical information for breeding programs, a sequencing project is underway to finalize a reference genome using a dihaploid line and a set of Menu Abstract: Dihaploid Coffea arabica Genome Sequencing and Assembly (Plant and Animal Genome XXIII Conference) https://pag.confex.com/pag/xxiii/webprogram/Paper16983.html [25/02/2015 15:00:12] 30 C. arabica accessions.

Caffeine is the most popular purine alkaloid, mainly found in coffees, teas, and cocoas. Caffeine content ranges from 0 to >3% and 0 to <1% dry matter basis in African and Indian Ocean Island (IOI) coffee beans, respectively. In Africa, eastern coastal species have low to medium caffeine content in their beans, whereas western and central species have medium to high levels. Despite exceptions in Africa and Madagascar, global trends in caffeine content show an increase progressing from east to west along the geographical distribution of the genus. The recessive allele of one gene controls caffeine absence, whereas global caffeine content is under polygenic control with strong genetic effects. For African species, the longer the flowering–fructification period, the higher the caffeine content. However, caffeine absence is not due to a short flowering–fructification period. IOI species show no correlation: all species of long flowering–fructification periods are caffeine-poor or caffeine-free, whereas the two medium/rich species have short flowering–fructification periods.

A recently proposed delimitation of the genus Coffea has raised new questions of geographical distribution, its evolutionary history, and mechanisms of its speciation. Global chromosome morphology and uniform C-banding patterns argue for a unique and common Coffea genome. However, evolution of the Coffea genus was associated with genome size variation and fine chromosomal changes (number of secondary constrictions, number and physical localization of rDNA loci and repetitive elements). The Coffea genome is small to medium-sized. Following the paleo-ancestral hexaploidization common to all dicotyledons, it did not undergo a whole-genome duplication. Although genus size variation did not provoke strong variations of the genome structure, it has played a role in its genus speciation. Indeed, the higher the difference in genome size of two species, the less likely they could be intercrossed. On a molecular scale, transposable element-insertion patterns produced complementary chronological information related to the events that shaped the evolutionary history of genus Coffea.

The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated.Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species.Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity.Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.

Coffee seed conservation biology: Fundamental aspects and practical implications. A review Since the early 1990s, the coffee seed has been: designated by several international laboratories as the model system for studying the physiology of seeds of the "intermediate" category. In contrast to orthodox seeds, longevity of which increases when they are dehydrated and stored at low temperature, intermediate seeds are only partially tolerant to desiccation and low temperatures. In the narrow ranges of water contents and temperatures which can thus be used, the longevity of intermediate seeds remains very short, which constitutes a major limitation for the conservation of the biodiversity of these species. The development of new analytical chemistry techniques made it possible to demonstrate that the poor longevity of coffee seeds was associated with several types of cellular damage : neutral lipid hydrolysis leading to the accumulation of free fatty acids(e-) which destabilize membranes, selective loss of a class of phospholipids, loss and oxidation(t-) of the two major hydrophilic antioxidants, ascorbic acid and glutathione. Thanks to the knowledge gained on the processes involved in coffee seed ageing, we propose for the first time in this paper highly accurate technical recommendations for the preparation and the short-term storage of seed lots. Meanwhile, through biophysical approaches including differential scanning calorimetry, the understanding of the mechanisms involved in coffee seed tolerance to ultra-low temperature exposure has significantly progressed. Based on this knowledge, a very effective cryopreservation technique has been developed for coffee seeds, facilitating the long-term conservation of Coffea genetic resources.

BACKGROUND AND AIMSThe phenolic composition of Coffea leaves has barely been studied, and therefore this study conducts the first detailed survey, focusing on mangiferin and hydroxycinnamic acid esters (HCEs).METHODSUsing HPLC, including a new technique allowing quantification of feruloylquinic acid together with mangiferin, and histochemical methods, mangiferin content and tissue localization were compared in leaves and fruits of C. pseudozanguebariae, C. arabica and C. canephora. The HCE and mangiferin content of leaves was evaluated for 23 species native to Africa or Madagascar. Using various statistical methods, data were assessed in relation to distribution, ecology, phylogeny and use.KEY RESULTSSeven of the 23 species accumulated mangiferin in their leaves. Mangiferin leaf-accumulating species also contain mangiferin in the fruits, but only in the outer (sporophytic) parts. In both leaves and fruit, mangiferin accumulation decreases with ageing. A relationship between mangiferin accumulation and UV levels is posited, owing to localization with photosynthetic tissues, and systematic distribution in high altitude clades and species with high altitude representatives. Analyses of mangiferin and HCE content showed that there are significant differences between species, and that samples can be grouped into species, with few exceptions. These data also provide independent support for various Coffea lineages, as proposed by molecular phylogenetic analyses. Sampling of the hybrids C. arabica and C. heterocalyx cf. indicates that mangiferin and HCE accumulation may be under independent parental influence.CONCLUSIONSThis survey of the phenolic composition in Coffea leaves shows that mangiferin and HCE accumulation corresponds to lineage recognition and species delimitation, respectively. Knowledge of the spectrum of phenolic accumulation within species and populations could be of considerable significance for adaptation to specific environments. The potential health benefits of coffee-leaf tea, and beverages and masticatory products made from the fleshy parts of Coffea fruits, are supported by our phenolic quantification.

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.

Coffee seed conservation biology: Fundamental aspects and practical implications. A reviewSince the early 1990s, the coffee seed has been: designated by several international laboratories as the model system for studying the physiology of seeds of the "intermediate" category. In contrast to orthodox seeds, longevity of which increases when they are dehydrated and stored at low temperature, intermediate seeds are only partially tolerant to desiccation and low temperatures. In the narrow ranges of water contents and temperatures which can thus be used, the longevity of intermediate seeds remains very short, which constitutes a major limitation for the conservation of the biodiversity of these species. The development of new analytical chemistry techniques made it possible to demonstrate that the poor longevity of coffee seeds was associated with several types of cellular damage : neutral lipid hydrolysis leading to the accumulation of free fatty acids(e-) which destabilize membranes, selective loss of a class of phospholipids, loss and oxidation(t-) of the two major hydrophilic antioxidants, ascorbic acid and glutathione. Thanks to the knowledge gained on the processes involved in coffee seed ageing, we propose for the first time in this paper highly accurate technical recommendations for the preparation and the short-term storage of seed lots. Meanwhile, through biophysical approaches including differential scanning calorimetry, the understanding of the mechanisms involved in coffee seed tolerance to ultra-low temperature exposure has significantly progressed. Based on this knowledge, a very effective cryopreservation technique has been developed for coffee seeds, facilitating the long-term conservation of Coffea genetic resources.