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Update on Cacao Genome Sequencing Project

The Cacao Genome Sequencing Project has made significant strides from June 2008 to June 2009. Achievements include the completion of the physical map at Clemson University, the draft genome sequence of Matina 1-6 produced by USDA-ARS, and the ongoing production of a 20 kb paired-end library at Roche, Inc. Further developments involve the initial assembly of the draft sequence by the Joint Genome Institute and transcriptome sequencing completed. A genome sequence database has been established to facilitate access to data and publications related to cacao genetics.

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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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