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Update on Cacao Genome Sequencing Project

Update on Cacao Genome Sequencing Project. August 4, 2009 NCGR, Santa Fe, NM. Overall Plan for Year 1 June 2008 – June 2009 (prepared November 21, 2008).

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Update on Cacao Genome Sequencing Project

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  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.

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