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Title: Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon

Author
item TYLER, LUDMILA - University Of California
item Bragg, Jennifer
item WU, JIAJIE - University Of California
item YNG, XIACHAN - Oak Ridge National Laboratory
item TUSKAN, GERALD - Oak Ridge National Laboratory
item Vogel, John

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2010
Publication Date: 10/25/2010
Citation: Tyler, L., Bragg, J.N., Wu, J., Yng, X., Tuskan, G., Vogel, J.P. 2010. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. Biomed Central (BMC) Genomics. 11:600.

Interpretive Summary: Glycoside hydrolases are a group of enzymes that cleave the bond between a carbohydrate and another molecule. Glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. We annotated the glycoside hydrolase genes in the newly sequenced model grass Brachypodium distachyon and in sorghum. We then compared the glycoside hydrolases in several grasses and dicots to gain a broader understanding of the evolution and function of this large class of genes. This work sets the stage for future experiments that address the role of the large gene family in plant growth and development.

Technical Abstract: Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, both at the whole-genome level and at the level of individual glycoside hydrolase families. We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. Examination of individual glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51) revealed both similarities and distinctions between monocots and dicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a monocot model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.