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Published on November 10, 2006; 10.1104/pp.106.087262

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Received July 24, 2006
Accepted October 22, 2006

Combining Expression and Comparative Evolutionary Analysis. The COBRA Gene Family

Siobhan M. Brady , Shuang Song , Kanwarpal Dhugga , J. Antoni-Rafalski , and Philip N. Benfey *

Department of Biology and The Institute for Genome Sciences and Policy, Duke University, Box 91000, Durham, NC 27708, USA
Syngenta Biotechnology, Inc., P. O. Box 12257, 3054 East Cornwallis Road, Research Triangle Park, NC 27709, USA
Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, Johnston, IA, 50131-1004, USA
Genetic Discovery Group, DuPont Crop Genetics Research, DuPont Experimental Station Building E353, Wilmington, DE, 198803, USA

* Corresponding author; email: philip.benfey{at}duke.edu.

Plant cell shape is achieved through a combination of oriented cell division and cell expansion and is defined by the cell wall. One of the genes identified to influence cell expansion in the Arabidopsis thaliana root is the COBRA gene which belongs to a multigene family. Three members of the AtCOBRA gene family have been shown to play a role in specific types of cell expansion, or cell wall biosynthesis. Functional orthologs of one of these genes have been identified in maize and rice (Schindelman et al., 2001; Li et al., 2003; Brown et al., 2005; Persson et al., 2005; Ching et al., 2006; Jones et al., 2006). We present the maize counterpart of the COBRA gene family, and the COBRA gene superfamily phylogeny. Most of the genes belong to a family with two main clades as previously identified by analysis of the Arabidopsis family alone. Within these clades, however, clear differences between monocot and eudicot family members exist and these are analyzed in the context of Type I and Type II cell walls in eudicots and monocots. In addition to changes at the sequence level, gene regulation of this family in a eudicot, Arabidopsis, and a monocot, maize is also characterized. Gene expression is analyzed in a multivariate approach, using data from a number of sources including MPSS libraries, transcriptional reporter fusions, and microarray data. This analysis has revealed that the expression of Arabidopsis and maize COB gene family members is highly developmentally and spatially regulated at the tissue and cell type-specific level, and that gene superfamily members show overlapping and unique expression patterns and only a subset of gene superfamily members act in response to environmental stimuli. Regulation of expression of the Arabidopsis COB gene family members has highly diversified in comparison to that of the maize COB gene superfamily members. We also identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of AtCOB.




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