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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #274375
Title: Transcriptome characterization for genome annotation and functional genomics in Theobroma cacao

Author
item MOCKAITIS, KEITHANNE - Indiana University
item GILBERT, DON - Indiana University
item MAY, GREG - National Center For Genome Resources
item PODICHETI, RAM - Indiana University
item SMITH, ZACHARY - Indiana University
item FORD, JAMES - Indiana University
item Royaert, Stefan
item MARELLI, JEAN - M & M Mars Company - Brazil
item CAHOON, EDGAR - University Of Nebraska
item Kuhn, David
item Schnell Ii, Raymond
item MOTAMAYOR, JUAN - Mars, Inc

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2011
Publication Date: 1/16/2011
Citation: Mockaitis, K., Gilbert, D., May, G., Podicheti, R., Smith, Z.M., Ford, J.B., Royaert, S.E., Marelli, J.P., Cahoon, E.B., Kuhn, D.N., Schnell II, R.J., Motamayor, J.C. 2011. Transcriptome characterization for genome annotation and functional genomics in Theobroma cacao. Annual International Plant & Animal Genome Conference. 2011.

Interpretive Summary:

Technical Abstract: Evidence from leaf transcriptome sequencing using two technology platforms, in combination with protein homology and trained ab initio predictions, previously enabled us to build 35,000 gene models in T. cacao (www.cacaogenomedb.org). Here we review the contribution of each data type to cacao gene annotation. Since the genome is the first of the Malvaceae to be sequenced, the notable fraction of cacao gene models built from experimental evidence alone provides a first look into functional novelty in this family. Transcriptome sequencing since our September 15, 2010 genome release has provided evidence for additional gene models. Original floral and bean collections have contributed substantially to gene discovery, and we present an overview of specific cacao transcriptomes sequenced and characterized to date. Recent experiments involving extensive additional sequencing include surveys of transcript accumulation in pistils during fertilization, and in beans during early development.