Maize Metabolic Network Construction and Transcriptome Analysis

Marcela K. Monaco

doi:10.3835/plantgenome2012.09.0025

Maize Metabolic Network Construction and Transcriptome Analysis

2013-03-01

83

OA

AI

Palitha Dharmawardhana

Ethalinda K. S. Cannon

DOI：10.3835/plantgenome2012.09.0025

Original

Save

View PDF

Abstract

En 中文

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 L. subsp. 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 maize reference genome sequenced from the B73 variety. MaizeCyc version 2.0.2 is a collection of 391 maize pathways involving 8889 enzyme mapped to 2110 reactions and 1468 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. We found that 1062 differentially expressed metabolic genes mapped to 524 unique enzymatic reactions associated with 310 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 (Oryza sativa L.) and Arabidopsis thaliana (L.) Heynh. against the PathoLogic module of Pathway Tools. The network and the database that were also developed as a community resource are freely accessible online at http://maizecyc.maizegdb.org to facilitate analysis and promote studies on metabolic genes in maize.

Keywords:

BIOCHEMICAL PATHWAY DATABASE

BUNDLE-SHEATH

PLANT

GENOME

EVOLUTION

MODEL

C-4

MESOPHYLL

COMMUNITY

ONTOLOGY

Maize Metabolic Network Construction and Transcriptome Analysis

Abstract

AI Summary

Journal

Organization