Open Access Research article

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

Fuyu Xu1, Myoung-Ryoul Park1, Ai Kitazumi1, Venura Herath14, Bijayalaxmi Mohanty2, Song Joong Yun3 and Benildo G de los Reyes1*

Author Affiliations

1 School of Biology and Ecology, University of Maine, 5735 Hitchner Hall, Orono, ME, 04469, USA

2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore, 117576

3 Department of Crop Science and Institute of Agricultural Science and Technology, Chonbuk National University, Chonju, 561-756, Korea

4 Present Address: Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka, 20400

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BMC Genomics 2012, 13:497  doi:10.1186/1471-2164-13-497

Published: 20 September 2012

Additional files

Additional file 1:

Phylogenetic reconstruction of orthologous and paralogous bZIP transcription factors in Oryza sativa (Os), Sorghum bicolor (Sb) and Arabidopsis thaliana (At).

Format: PPTX Size: 201KB Download file

Open Data

Additional file 2:

List of total TFBS classes detected among orthologs and paralogs through the Genomatix promoter detection algorithm. Annotation is based on Genomatix and TRANSFAC databases.

Format: XLS Size: 41KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Frequency of occurrence of the ortholog-specific TFBS classes in different COGs.

Format: PPTX Size: 197KB Download file

Open Data

Additional file 4:

Frequency of occurrence of the ortholog-specific TFBS classes in different COGs.

Format: PPTX Size: 196KB Download file

Open Data

Additional file 5:

Binary hierarchical dendogram showing the clustering patterns for TFBS classes that are common between the stress-associated orthologs and their non-stress-associated paralogs. The associated transcriptional regulators (TF) and their known biological functions based on the annotation in the plant-specific cis-element (Genomatix, TRANSFAC and PLACE) databases are shown for each TFBS class.

Format: PPTX Size: 99KB Download file

Open Data

Additional file 6:

Binary hierarchical dendogram showing the clustering patterns of ortholog-specific TFBS classes. TFBS classes shown are found among the members of the tri-species COGs but not among their paralogs. The associated transcriptional regulators (TF) and their known biological functions based on the annotation in the plant-specific cis-element (Genomatix, TRANSFAC and PLACE) databases are shown for each TFBS class.

Format: PPTX Size: 140KB Download file

Open Data