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Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle

Julietta Jupe12, Remco Stam123, Andrew JM Howden12, Jenny A Morris23, Runxuan Zhang4, Pete E Hedley23* and Edgar Huitema12*

Author Affiliations

1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, UK

2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK

3 Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK

4 Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK

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Genome Biology 2013, 14:R63  doi:10.1186/gb-2013-14-6-r63

Published: 25 June 2013

Additional files

Additional file 1:

Table S1. Phytophthora capsici genes encoding putative secreted proteins found expressed in microarray experiments. Lists of P. capsici genes encoding candidate secreted proteins are given. These represents gene for which expression was detected in the infectious and in vitro stages.

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Additional file 2:

Table S2. PcHmp1, PcNPP1, and PcCdc14 coregulated genes Overview of genes found to be coregulated with marker genes in Phytophthora capsici. Gene identifier, probe ID number, and normalized expression value (fold change over mean expression) are given for each gene and at each time point. Gene Ontology (GO) annotations are also given for each gene where available.

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Additional file 3:

Table S3. Significantly enriched ontologies coregulated with marker genes, Overview of gene ontologies that are significantly enriched in the fractions that are specifically coregulated with P. capsici marker genes as shown in Figure 3C. Gene Ontology (GO) terms, P-values, false discovery rates (FDRs), and query and reference sample sizes are given.

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Additional file 4:

Table S4. Phytophthora capsici candidate RXLR genes expressed in microarray experiments. Overview of RXLR effector genes found to be upregulated during specific lifecycle stages in P. capsici. Gene identifier, probe ID number, and normalized expression value (fold change over mean expression) are given for each gene and at each time point. Genes are listed per class as shown in Figure 4.

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Additional file 5:

Table S5. Annotation and expression of tomato genes differentially expressed in pairwise comparisons. Overview of genes found to be differentially expressed between timepoints during Phytophthora capsici infection. Gene identifiers, normalized expression values, and Gene Ontology (GO) annotations are given.

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Additional file 6:

Table S6. Tomato genes differentially expressed in each pairwise comparison. Overview of genes found to be differentially expressed during Phytophthora capsici infection in pairwise comparisons between two timepoints. Gene identifiers and normalized expression values are given.

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Additional file 7:

Table S7. Genes corresponding to enriched gene ontologies (GOs) in pairwise comparisons. Overview of GOs that were significantly enriched in the fractions that were specifically upregulated or downregulated between two time points as shown in Figure 6. GOs, P-values, false discovery rates (FDRs), and query and reference sample sizes are given.

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Additional file 8:

Table S8. Tomato genes with possible roles in pathogen-associated molecular pattern (PAMP) perception and signaling, differentially expressed during Phytophthora capsici infection. Overview of candidate PAMP signaling and transcription-factor genes found to be differentially expressed during P. capsici infection. Gene identifiers, normalized expression values, and annotations are given. Genes are grouped based on their expression patterns as shown in Figure 7 and 8 respectively.

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Additional file 9:

Table S9. Putative RXLR effectors used in this study. Overview of putative RXLR effectors. Gene name, probe ID, and nucleotide sequence are given for each gene.

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Additional file 10:

Figure S1. Assessment of cell viability during Phytophthora capsici infection. Transgenic Nicotiana benthamiana plants constitutively expressing ER-eGFP, a green fluorescent protein (GFP) localized to the endoplasmic reticulum (ER) were used to assess whether host cells were alive during the course of infection. (A) Photographs of N. benthamiana leaves infected with zoospore suspensions of P. capsici at 0, 8, 24, 48, and 72 hpi. (B) Confocal microscopy images of N. benthamiana leaves infected with a transgenic P. capsici strain expressing the fluorescent protein TdTomato. Within the first 24 hours, the host ER was largely intact despite the presence of P. capsici, and haustoria were often seen to invaginate living cells. After 24 hours, the ER network was disrupted as shown by the unstructured distribution of GFP, suggesting dead or dying cells. Bar = 20 μm.

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Additional file 11:

Figure S2. Reverse transcription PCR verification of marker-gene expression during infection. Expression of the marker genes PcHmp1, PcNpp1, PcCdc14, and PcTub (constitutive control) was tested by semi-quantitative PCR on cDNA derived from a time-course infection series used for the microarrays. Amplification of genes on cDNA derived from water-inoculated control (non-infected; ni) and tomato harvested 0, 8, 16, 24, 48, and 72 hpi with Phytophthora capsici.

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