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The wild species of the Coffea genus present a very wide morphological, genetic, and biochemical diversity. Wild species are recognized more resistant to diseases, pests, and environmental variations than the two species currently cultivated worldwide: C. arabica (Arabica) and C. canephora (Robusta). Consequently, wild species are now considered as a crucial resource for adapting cultivated coffee trees to climate change. Within the Coffea genus, 79 wild species are native to the Indian Ocean islands of Comoros, Mayotte, Mauritius, Réunion and Madagascar, out of a total of 141 taxa worldwide. Among them, a group of 9 species called "Baracoffea" are particularly atypical in their morphology and adaptation to the sandy soils of the dry deciduous forests of western Madagascar. Here, we have attempted to shed light on the evolutionary history of three Baracoffea species: C. ambongensis, C. boinensis and C. bissetiae by analyzing their chloroplast and nuclear genomes. We assembled the complete chloroplast genomes de novo and extracted 28,800 SNP (Single Nucleotide Polymorphism) markers from the nuclear genomes. These data were used for phylogenetic analysis of Baracoffea with Coffea species from Madagascar and Africa. Our new data support the monophyletic origin of Baracoffea within the Coffea of Madagascar, but also reveal a divergence with a sister clade of four species: C. augagneurii, C. ratsimamangae, C. pervilleana and C. Mcphersonii (also called C. vohemarensis), belonging to the Subterminal botanical series and living in dry or humid forests of northern Madagascar. Based on a bioclimatic analysis, our work suggests that Baracoffea may have diverged from a group of Malagasy Coffea from northern Madagascar and adapted to the specific dry climate and low rainfall of western Madagascar. The genomic data generated in the course of this work will contribute to the understanding of the adaptation mechanisms of these particularly singular species. [ABSTRACT FROM AUTHOR]

Abstract Background Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. Results Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. Conclusions These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain divergences. Our results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy.

Abstract Background In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae. Description MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three Coffea species/hybrids. Microsatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database). Conclusion We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.

Abstract Background Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone. Results Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals. Conclusion Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.

Abstract Background Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of ≈ 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. Results This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. Conclusion This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.