Progress on the preliminary sequence of the Coffea canephora genome

Aldexandre de Kochko, Diversité et Adaptation des Plantes Cultivées
Victor Albert, University of Buffalo
Alan C. Andrade, Recursos Genéticos e Biotecnologia, Brazil
Giovanni Giuliano, ENEA Casaccia Research Center, Italy
Giorgio Graziosi, Universita di Trieste
Robert J. Henry, Southern Cross University
Ray Ming, University of Illinois at Urbana-Champaign
Chifumi Nagai, Hawaii Agriculture Research Center (HARC)
Steve Rounsley, University of Arizona
David Sankoff, University of Ottawa

Abstract

An international consortium of 10 laboratories from 6 countries started the sequencing of the diploid species Coffea canephora during the second semester of 2009. The genus Coffea is a member of the family Rubiaceae, one of the largest among angiosperms, mainly represented in tropical areas, and a member of the Asterid clade. Interestingly, although coffee is the second most valuable commodity exported by developing countries, ours is the first known effort to get a broad view of its genome sequence. Based on deep sequencing technologies, the genome of a double haploid plant was used for performing 12 runs with the Roche Titanium technology and 1 run with the Illumina G2 technology. Available sequences in public data banks were used to help the assembly of the obtained sequences. We expect to obtain an assembly sufficient enough to allow an assessment of the general organization of the genome, to permit comparisons with existing sequenced genomes, and to lead to better understanding of Coffea genome evolution. Identification of the great majority of genes should provide insight into specific metabolic and developmental pathways. A dramatic increase in the quantity of genetic markers will also be provided, permitting the establishment of more dense genetic maps for C. arabica. Identification of transposable elements and analysis of their distribution will also be greatly facilitated.