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BIOINFORMATICS

A Dynamic Interface for Capsaicinoid Systems Biology^{1,[C],[W],[OA]}

Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853 (M.M.); SOL Genomics Network, Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (A.P., L.M.); Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel (Y.B., I.P.); and College of Agriculture and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706 (M.M.J.)

Capsaicinoids are the pungent alkaloids that give hot peppers (Capsicum spp.) their spiciness. While capsaicinoids are relatively simple molecules, much is unknown about their biosynthesis, which spans diverse metabolisms of essential amino acids, phenylpropanoids, benzenoids, and fatty acids. Pepper is not a model organism, but it has access to the resources developed in model plants through comparative approaches. To aid research in this system, we have implemented a comprehensive model of capsaicinoid biosynthesis and made it publicly available within the SolCyc database at the SOL Genomics Network (http://www.sgn.cornell.edu). As a preliminary test of this model, and to build its value as a resource, targeted transcripts were cloned as candidates for nearly all of the structural genes for capsaicinoid biosynthesis. In support of the role of these transcripts in capsaicinoid biosynthesis beyond correct spatial and temporal expression, their predicted subcellular localizations were compared against the biosynthetic model and experimentally determined compartmentalization in Arabidopsis (Arabidopsis thaliana). To enable their use in a positional candidate gene approach in the Solanaceae, these genes were genetically mapped in pepper. These data were integrated into the SOL Genomics Network, a clade-oriented database that incorporates community annotation of genes, enzymes, phenotypes, mutants, and genomic loci. Here, we describe the creation and integration of these resources as a holistic and dynamic model of the characteristic specialized metabolism of pepper.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Michael Mazourek (mm284{at}cornell.edu).

^[C] Some figures in this article are displayed in color online but in black and white in the print edition.

^[W] The online version of this article contains Web-only data.

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www.plantphysiol.org/cgi/doi/10.1104/pp.109.136549

^* Corresponding author; e-mail mm284{at}cornell.edu.

Received February 2, 2009; accepted June 13, 2009; published June 24, 2009.

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