The International Coffea Genome13 Project: A Way to Understand the Evolutionary History of Coffea Genomes and Unlock the Potential Use of Wild Species in Breeding?

Comparative genomics between cultivated and wild species at the genus scale is a powerful tool to understand the evolutionary history of genomes and to unlock the genetic use of wild species in breeding programs. The recent availability of the Coffea canephora (Robusta coffee) genome allows for the first time an investigation of genome composition and evolution at the genus scale for tropical trees. Coffea genus (Rubiaceae) contains 124 species natives to inter-tropical forests of Africa, Indian Ocean islands, Indian sub-continent and Australasia. Only two African are cultivated. Wild species grow in contrasting environments suggesting that they represent a potential source of diversity and a rich reservoir of genes for improving the world's most widely traded agricultural commodity.  Based on a robust phylogenetic framework, we selected 13 diploid Coffea species with diverse geographical origins, environmental adaptations and genome sizes. All species were sequenced with the 454 (0.1X) and the Illumina technology (20X). The reads obtained were assembled into contigs and compared to the C. canephora reference genome sequence.  These resources have allowed study of the maternal molecular phylogeny using chloroplast genome reconstruction and plastid insertion into the nuclear genomes. They will serve also as starting points to tackle among other issues, the origin of genome size variations, the evolutionary dynamics of transposable elements and non coding elements, the overall allelic diversity and the diversity of metabolic pathways that could be of interest for breeding targets especially to increase the sensory variability of the final product. The first results will be presented.