Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

Theobroma cacao Genome Sequencing And Assembly Strategy Evaluation

F Alex Feltus^1,2 , Barbara Blackmon¹ , Stephen P Ficklin¹ , Niina Haiminen³ , David N Kuhn⁴ , Greg D May⁵ , Juan-Carlos Motamayor⁶ , Chris A Saski¹ , Ray J Schnell⁴ , Margaret E Staton¹

¹  Clemson University Genomics Institute, Clemson, SC, 29634, USA

²  Clemson University Department of Genetics & Biochemistry, Clemson, SC, 29634, USA

³  IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA

⁴  USDA-ARS Subtropical Horticulture Research Station (SHRS), Miami, FL, 33158, USA

⁵  National Center for Genome Resources, Santa Fe, NM, 87505, USA

⁶  Mars Incorporated, McLean, VA, 22101, USA

The Clemson University Genomics Institute (CUGI) is performing a proof of concept pilot assembly of a subset of the minimum tiling path (MTP) derived from the cacao physical map that contains genes of interest to the cacao community. BAC clones have been selected for sequencing that cover this pilot 3 Mbp region of the MTP. MTP BAC clones are being sequenced using pooled BAC shotgun 454/Roche reads, pooled BAC shotgun Illumina/Solexa reads, and a traditional BAC-by-BAC Sanger sequenced shotgun library approach. Once sequencing is complete, assembly of the MTP will be performed on these reads with varying levels of coverage and read-type mixtures in order to determine the optimal read depth and flavors required for efficient assembly. In addition, we will use the BAC-end sequences distributed every ~20 Kbp within the 3 Mbp segment, genetic marker sequences, and RNA-seq clusters to scaffold and merge contigs. In parallel, CUGI is performing assembly simulations with in silico generated data that mimics 3 MBp of the cacao genome generated by IBM scientists to evaluate various assemblies from Sanger, 454, and Solexa data to determine the needed pool size, appropriate level of barcoding, error tolerance, and most efficient mix of read types. Information gathered in the successful assembly of the pilot region will guide the overall Theobroma cacao genome sequencing strategy.