Research article
Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots
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* Corresponding author: Dierk Wanke dierk.wanke@zmbp.uni-tuebingen.de
1 Department of Plant Biology and Forest Genetics, The Swedish University of Agricultural Sciences (SLU), P.O. Box 7080, SE-750 07 Uppsala, Sweden
2 Center of Plant Molecular Biology (ZMBP), University of Tuebingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germany
3 CELISCA (Center for Life Science Automation), Friedrich-Barnewitz-Strasse 8, D-18119 Rostock, Germany
4 Lawrence Berkeley Laboratory, Earth Science Division, 1 Cyclotron Rd., Berkeley, CA 94720, USA
BMC Genomics 2008, 9:194 doi:10.1186/1471-2164-9-194
Published: 28 April 2008Additional files
Additional File 1:
Multiple alignment of WRKY_GCM1-like domains. Multiple alignment of WRKY_GCM1-like domain amino acid sequences from Arabidopsis (AtWRKY), barley (HvWRKY), rice (OsWRKY), Physcomitrella (PpWRKY), Dictyostelium discoideum (DdWRKY), Giardia lamblia (GlWRKY),Homo sapiens (HsFLYWCH) and Mus musculus (MmFLYWCH). N-terminal and C-terminal WRKY domains of group 1 WRKY proteins are indicated as _N and _C, respectively. The conserved WRKY signature is highlighted in bold letters, the amino acids forming the zinc-finger motif are shaded with grey, gaps in the alignment are indicated by dashes.
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Additional File 2:
Phylogenetic tree based on all WRKY_GCM1-like domains considered in the Alignment of Additional File 1. Phylogenetic tree based on the WRKY domain amino acid sequences given in Additional Figure 1. Sequences of Arabidopsis (AtWRKY), barley (HvWRKY), Physcomitrella (PpWRKY), rice (OsWRKY), Dictyostelium discoideum (DdWRKY), Giardia lamblia (GlWRKY) Homo sapiens (HsFLYWCH) and Mus musculus (MmFLYWCH) are arranged in clusters with the zinc finger domain of the Arabidopsis mutator-like transposase (AtMutTrans) as outgroup. Tree topology has been confirmed by using three different programs. Bootstrap values from 1000 iterations and bigger than 500 are included in the tree. HvWRKY sequences are highlighted in bold letters. Groups and subgoups of WRKY1 to 3 are indicated by bars on the right side.
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Additional File 3:
Normalized signal intensities of HvWRKY genes, AtWRKY genes and a set of 101 randomly chosen gene pairs. The table contains all essential data for the comparative gene expression analysis for barley and Arabidopsis WRKY genes as well as control gene pairs on the extracted subsets of the microarray expression datasets of homologous organs by Druka et al. [36] and Schmid et al. [37].
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Additional File 4:
Signal intensities of RT-PCR experiment with barley, Arabidopsis and rice WRKY genes. Tables contain raw signal intensity values of bands from RT-PCR experiments shown in Figure 5.
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Additional File 5:
Distribution of the relative correlation coefficient in randomly chosen and HvWRKY-AtWRKY gene pairs. The relative correlation coefficient was calculated from the normalized signal intensities of the gene pairs and plotted according to its occurrence. Random gene pairs exhibited an average correlation coefficient of 0.01. WRKY gene pairs exhibited a divided curve with two maxima. When only the best pairing orthologs were considered, the first peak of more random distribution is lost.
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Additional File 6:
Primer sequences used in RT-PCR experiment with barley, Arabidopsis and rice WRKY genes. Table containing the sequences of primers, numbers of cycles and expected fragment size of RT-PCR experiments depicted in Figure 5.
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