Plant & Animal Genomes XVIII Conference Plant & Animal Genomes XVIII ConferenceJanuary 9-13, 2010
Town & Country Convention Center
San Diego, CA
Keithanne Mockaitis1 , David Kuhn2 , Mohammed Mohiuddin3 , Chinnappa Kodira3 , Dorrie Main4 , Niina Haiminen5 , Greg May6 , Chris Saski7 , Brian Scheffler8 , Raymond J. Schnell2 , Tim Harkins9 , Juan Carlos Motamayor10 , Howard Shapiro10
To compliment the T. cacao genome sequencing initiative and to build a reference set of expressed genes for functional studies, a broad and state-of-the-art approach to transcriptome sequencing is underway. Using newly optimized methods, transcriptome sequencing libraries were prepared from RNA of organ-specific collections of Matina1-6, the chosen cacao genome sequence reference. De novo assemblies were generated using a newly released version of the 454 Newbler Assembler for cDNA analysis.
Analysis of 1.5 M reads from 454 GS-FLX Titanium sequencing of a Matina1-6 leaf transcriptome library produced an assembly of 22,172 isotigs, representing individual transcripts of the reference tree. Earlier 159,320 cloned EST sequences derived from a variety of genotypes and tissue collections were assembled into 45,056 putative unigenes using CAP3 (Huang and Madan, 1999). Deep surveys of RNA samples from Matina1-6 and more highly polymorphic accessions were generated from Illumina GAII sequencing reads mapped to the above assemblies. Findings from these projects, additional 454 and Illumina mRNA sequencing results, as well as protein-coding functional annotation, will be presented to overview current collaborative efforts engaged in cacao gene discovery.