The WRKY transcription factor family in Brachypodium distachyon
1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
2 Institute for Green Energy and Clean Environment, Charlottesville, VA, 22906, USA
BMC Genomics 2012, 13:270 doi:10.1186/1471-2164-13-270Published: 22 June 2012
Additional file 1:
Figure S1. Combined phylogenetic tree of the WRKY transcription factor families in Brachypodium, Arabidopsis, rice, and Physcomitrella patens, together with published WRKY transcription factors from wheat. All WRKY transcription factors are labeled and all bootstrap values indicated. The WRKY domains were used to infer the evolutionary history of the WRKY family using the Neighbor-Joining method. The WRKY domain from a WRKY transcription factor found in a fungus belonging to the Zygomycete class, Mucor circinelloides, was included as a distant root (blue dot). Brachypodium and wheat proteins are indicated by red and green dots, respectively. The WRKY subfamilies are indicated. I-N and I-C indicate the N-terminal and C-terminal domains from Group I WRKY proteins. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. Phylogenetic analyses were conducted in MEGA4  and MEGA5 . The distance scale (0.1) is shown.
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Additional file 2:
Figure S2. The number of predicted WRKY transcription factors in Brachypodium found in four different databases. The first number in brackets indicates the predicted number of functional genes and the second number the predicted total of pseudogenes.
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Additional file 3:
Table S1. The presence or absence of the 86 WRKY transcription factors from Brachypodium in four different databases. The name of the corresponding gene model is indicated and if no gene model is present, that is also shown. An N indicates that the WRKY transcription factor is not presence in the database.
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Additional file 4:
Table S1. The WRKY transcription factor family in Brachypodium. For each WRKY transcription factor, the chromosomal location and gene model (if present) are shown, together with any comments concerning the gene. For each protein, a cartoon of the domain structure is also shown to facilitate comparisons of similar proteins. The domain structure was producing using MEME and the complete amino acid sequences of all the family members were used.
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