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Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin. (Résumé d'auteur

A r t i c l e s Theobroma cacao L. is a diploid tree fruit species (2n = 2x = 20 (ref. 1)) endemic to the South American rainforests. Cocoa was domesticated approximately 3,000 years ago 2 in Central America 3. The Criollo cocoa variety, having a nearly unique and homozygous genotype, was among the first to be cultivated 4. Criollo is now one of the two cocoa varieties providing fine flavor chocolate. However, due to its poor agronomic performance and disease susceptibility, more vigorous hybrids created with foreign (Forastero) genotypes have been introduced. These hybrids, named Trinitario, are now widely cultivated 5. Here we report the sequence of a Belizean Criollo plant 6. Consumers have shown an increased interest for high-quality chocolate, and for dark chocolate, containing a higher percentage of cocoa 7. Fine-cocoa production is nevertheless estimated to be less than 5% of the world cocoa production due to the low productivity and disease susceptibility of the traditional fine-flavor cocoa varieties. Therefore, breeding of improved Criollo varieties is important for sustainable production of fine-flavor cocoa. 3.7 million tons of cocoa are produced annually (see URLs). However, fungal, oomycete and viral diseases, as well as insect pests, are responsible for an estimated 30% of harvest losses (see URLs). Like many other tropical crops, knowledge of T. cacao genetics and genomics is limited. To accelerate progress in cocoa breeding and the understanding of its biochemistry, we sequenced and analyzed the genome

Fruit provide essential nutrients and vitamins for the human diet. Not only is the lipid-rich fleshy mesocarp tissue of the oil palm (Elaeis guineensis) fruit the main source of edible oil for the world, but it is also the richest dietary source of provitamin A. This study examines the transcriptional basis of these two outstanding metabolic characters in the oil palm mesocarp. Morphological, cellular, biochemical, and hormonal features defined key phases of mesocarp development. A 454 pyrosequencingderived transcriptome was then assembled for the developmental phases preceding and during maturation and ripening, when high rates of lipid and carotenoid biosynthesis occur. A total of 2,629 contigs with differential representation revealed coordination of metabolic and regulatory components. Further analysis focused on the fatty acid and triacylglycerol assembly pathways and during carotenogenesis. Notably, a contig similar to the Arabidopsis (Arabidopsis thaliana) seed oil transcription factor WRINKLED1 was identified with a transcript profile coordinated with those of several fatty acid biosynthetic genes and the high rates of lipid accumulation, suggesting some common regulatory features between seeds and fruits. We also focused on transcriptional regulatory networks of the fruit, in particular those related to ethylene transcriptional and GLOBOSA/PISTILLATA-like proteins in the mesocarp and a central role for ethylene-coordinated transcriptional regulation of type VII ethylene response factors during ripening. Our results suggest that divergence has occurred in the regulatory components in this monocot fruit compared with those identified in the dicot tomato (Solanum lycopersicum) fleshy fruit model.