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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: Maize metabolic network construction and transcriptome analysis

item Monaco, Marcela -
item Sen, Taner
item Dharmawardhana, Palitha -
item Ren, Liya -
item Schaeffer, Mary
item Naithani, Sushma -
item Amarasinghe, Vindhya -
item Thomason, Jim -
item Harper, Elisabeth
item Gardiner, Jack -
item Cannon, Ethalinda -
item Lawrence, Carolyn
item Ware, Doreen
item Jaiswal, Pankaj -

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 20, 2012
Publication Date: March 8, 2013
Citation: Monaco, M.K., Sen, T.Z., Dharmawardhana, P., Ren, L., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Gardiner, J.M., Lawrence, C.J., Ware, D., Jaiswal, P., Naithani, S., Cannon, E. 2013. Maize metabolic network construction and transcriptome analysis. The Plant Genome. 6(1):DOI:10.3835/plantgenome2012.09.0025.

Interpretive Summary: The Maize Genetics and Genomics Database (MaizeGDB) is the community resource for maize data and can be accessed online at The B73 maize genome is sequenced, and we now have a gene set placed on the genome. MaizeGDB already integrated a genome browser to its graphical user interface for easy viewing of the genome, gene sets, and other annotations. However, MaizeGDB was lacking a view where the genes are positioned in the metabolic pathway to which they belong. In order to address this need, we developed MaizeCyc, which is a genome-wide catalog of known and/or predicted metabolic and transport pathways. With the help of MaizeCyc, the maize researchers will be able to visualize their genes of interest in their metabolic context. MaizeCyc will therefore provide researchers a better understanding of the interactions between different genes that give rise to desired phenotypes, which in turn aids in creating better plants with optimal traits.

Technical Abstract: A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays ssp. mays (maize), we developed MaizeCyc a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant products, and other metabolites by annotating the genes identified in the B73 maize reference genome. MaizeCyc is a collection of 390 maize pathways involving 9,185 genes mapped to 2,177 reactions and 1,460 metabolites. We used MaizeCyc to describe the development and function of maize organs including leaf, root, anther, embryo and endosperm, by exploring the recently published microarray-based maize gene expression atlas (Sekhon et al., 2011). We found that 1,059 differentially expressed metabolic genes mapped to 513 unique enzymatic reactions associated with 308 pathways. The MaizeCyc pathway database was created by running a library of evidences collected from the maize genome annotation, gene based phylogeny trees and comparison to known genes and pathways from rice and Arabidopsis against the PathoLogic module of Pathway Tools. The network and the database are freely accessible online at to facilitate analysis and discovery of novel metabolic genes.

Last Modified: 7/25/2016
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