Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

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

Ludmila Tyler12, Jennifer N Bragg1, Jiajie Wu13, Xiaohan Yang4, Gerald A Tuskan4 and John P Vogel1*

Author Affiliations

1 USDA-ARS Western Regional Research Center, Albany, CA 94710, USA

2 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA

3 Department of Plant Sciences, University of California, Davis, CA 95616, USA

4 Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA

For all author emails, please log on.

BMC Genomics 2010, 11:600  doi:10.1186/1471-2164-11-600

Published: 25 October 2010

Additional files

Additional file 1:

Rice GHs. Rice GHs This file contains a FASTA-formatted list of protein sequences for rice GHs.

Format: TXT Size: 232KB Download file

Open Data

Additional file 2:

Arabidopsis GHs. Arabidopsis GHs This file contains a FASTA-formatted list of protein sequences for Arabidopsis GHs.

Format: TXT Size: 228KB Download file

Open Data

Additional file 3:

Identification of Brachypodium GHs. Identification of Brachypodium GHs This table contains the following information for each Brachypodium GH: the gene name, GH family assignment, Pfam-predicted domains, whether the Brachypodium protein matches a GH in rice or Arabidopsis, and the extent to which expression and splice-junction data support the gene model.

Format: DOC Size: 1022KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Modified Brachypodium GH models. Modified Brachypodium GH gene models This table lists the gene names, changes, and sequences associated with GH gene models which were modified or added relative to the v1.0 annotation.

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Brachypodium GHs. Brachypodium GHs This file contains a FASTA-formatted list of protein sequences for Brachypodium GHs.

Format: TXT Size: 196KB Download file

Open Data

Additional file 6:

Identification of Sorghum GHs. Identification of Sorghum GHs This table contains the following information for each sorghum GH: the gene name; the GH family assignment; the best E-value for a match to a Brachypodium, rice, or Arabidopsis GH; whether there is a Pfam-predicted GH domain; and the protein sequence.

Format: XLS Size: 263KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Sorghum GHs. Sorghum GHs This file contains a FASTA-formatted list of protein sequences for sorghum GHs.

Format: TXT Size: 204KB Download file

Open Data

Additional file 8:

GH Summary. GH Summary This table lists the number of GHs in each family in Arabidopsis, rice, Brachypodium, and sorghum.

Format: XLS Size: 15KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Poplar GHs. Poplar GHs This table lists the abbreviated and full-length gene names, as well as the protein sequences, for selected poplar GHs analyzed in this study.

Format: XLS Size: 108KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

GH18 Rectangular Tree. GH18 Rectangular Tree This figure presents the same phylogenetic tree as Figure 3, but in a rectangular format, with complete bootstrap information and branch labels. The tree includes GH18 proteins from Arabidopsis, poplar, rice, Brachypodium, sorghum, and 18 other plants.

Format: PDF Size: 206KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 11:

Other Species. Other Species Included in Trees This table lists the abbreviated names, full scientific names, common names, and classifications of species included in the phylogenetic trees.

Format: XLS Size: 29KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

GH19 Rectangular Tree. GH19 Rectangular Tree This figure presents the same phylogenetic tree as Figure 4, but in a rectangular format, with complete bootstrap information and branch labels. The tree includes GH19 proteins from Arabidopsis, poplar, rice, Brachypodium, and sorghum.

Format: PDF Size: 98KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13:

GH5 Rectangular Tree. GH5 Rectangular Tree This figure presents the same phylogenetic tree as Figure 5, but in a rectangular format, with complete bootstrap information and branch labels. The tree includes GH5 proteins from Arabidopsis, poplar, rice, Brachypodium, sorghum, and 23 other species.

Format: PDF Size: 1.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 14:

GH28 Rectangular Tree. GH28 Rectangular Tree This figure presents the same phylogenetic tree as Figure 6, but in a rectangular format, with complete bootstrap information and branch labels. The tree includes GH28 proteins from Arabidopsis, poplar, rice, Brachypodium, sorghum, and maize.

Format: PDF Size: 3.1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 15:

GH51 Rectangular Tree. GH51 Rectangular Tree This figure presents the same phylogenetic tree as Figure 7, but in a rectangular format, with complete bootstrap information. The tree includes GH51 proteins from Arabidopsis, poplar, rice, Brachypodium, sorghum, and 14 other plants.

Format: PDF Size: 726KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 16:

GH13 Rectangular Tree. GH13 Rectangular Tree This figure presents the same phylogenetic tree as Figure 8, but in a rectangular format, with complete bootstrap information. The tree includes GH13 proteins from Arabidopsis, poplar, rice, Brachypodium, and sorghum.

Format: PDF Size: 85KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data