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Open Access Highly Accessed Research article

Phylogenetic and transcriptional analysis of an expanded bZIP transcription factor family in Phytophthora sojae

Wenwu Ye1, Yang Wang1, Suomeng Dong1, Brett M Tyler2 and Yuanchao Wang1*

Author Affiliations

1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China

2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA

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BMC Genomics 2013, 14:839  doi:10.1186/1471-2164-14-839

Published: 28 November 2013

Additional files

Additional file 1: Table S1:

Prediction pipeline statistics of bZIPs in oomycetes, diatoms, and fungi. Table S2 Details of predicted bZIP candidates in P. sojae. Table S3 Details of predicted bZIP candidates in other species. Table S4 Summary of HMMER search results from UniProtKB. Table S5 Primers for qRT-PCR assay.

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Additional file 2: Figure S1:

Predicted bZIP domains and α-helices of P. sojae bZIP candidates. The lines and blocks are proportional to the sequence lengths.

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Additional file 3: Figure S2:

Phylogenetic tree of bZIP domains from different species. The maximum-likelihood tree was constructed based on the protein sequences of the bZIP domains. Bootstrap values above 50 are shown near the tree nodes. The colors and shapes of gene labels refer to their species and bZIP domain class, respectively. Two C-R class proteins found in non-oomycete species are marked by asterisks and colored by pink.

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Additional file 4: Figure S3:

Phylogenetic trees built from different regions of P. sojae bZIP candidates. The trees were constructed using a maximum-likelihood method. Bootstrap values above 50 are shown at nodes. A, full-length proteins; B, bZIP domains; C, basic regions only; D, leucine zipper regions only.

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Additional file 5: Figure S4:

Phylogenetic tree from full length bZIP candidate proteins of P. sojae, P. infestans, and P. ramorum. The trees were constructed using a maximum-likelihood method. Bootstrap values above 50 are shown at nodes. The colors and shapes of gene labels refer to their species and bZIP domain class, respectively. The 1:1:1 orthologous clades and the species-specific clades are respectively marked by different colored stars.

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Additional file 6: Figure S5:

Relative expression levels of bZIP candidate genes following H2O2 treatment. Data of controls at 30 min (CK-0.5 h) were used as reference and normalized to 1.0 using P. sojae actA (GeneID: 108986) as a reference. Based on the treatment-control comparisons, asterisks indicate >1.2 fold elevation or -reductions respectively that are significant with a t-test P-value <0.05. A, Genes with reduced transcripts at one or more time-points. B, Genes that were not significantly regulated at any time-points. Histograms showing the digital gene expression profiling data from ten developmental and infection stages are shown on the right side of the H2O2 histogram for each gene. The data were averages of three independent replicates. Error bars indicate standard deviations.

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