1. Update on Cacao Genome Sequencing Project August 4, 2009 NCGR, Santa Fe, NM

2. Overall Plan for Year 1 June 2008 – June 2009 (prepared November 21, 2008) Physical map produced at Clemson University Genomics Institute (CUGI) by Chris Saski, Barbara Blackmon. Markers from the genetic map placed on physical map. COMPLETED Draft genome sequence (2x) of Matina 1-6 produced at USDA-ARS Stoneville on 454 machine by Brian Scheffler. COMPLETED 20 kb paired end library produced and sequenced at Roche, Inc. IN PROGRESS Initial assembly of 2x draft sequence by Joint Genome Institute (JGI) with Gerald Tuskan, Dan Rokhsar. Deeper sequencing depending on outcome of initial assembly. Low coverage sequencing of genomes of genetically diverse trees for SNP discovery. TRANSCRIPTOME SEQUENCING COMPLETED Genome sequence database and website constructed and ready for initial sequence information by Dorrie Main, Washington State University. COMPLETED

3. Details Physical Map: Candidate gene overgos. COSII overgos. 454 Sequencing: Pilot project and beyond. Assembly? Transcriptome sequence annotation and annotation update. Cacaogenomedb: Tools, access, publications and PIPRA.