Table S1. Raw and normalized data sets, and a list of regulated genes. Table S2. Symbiosis-regulated genes found in the seven different WCLUTO graph partitioning-based (GPB) clusters. Clustering analysis was carried out on the 395 symbiosis-regulated Pisolithus microcarpus and Eucalyptus globulus genes (ratios < 2.5 and > 0.4). Fig. S1. The Eucalyptus globulus?Pisolithus microcarpus in vitro Petri-dish system. Fig. S2. (a) The development of Eucalyptus?Pisolithus ectomycorrhiza synthesized in vitro.. (b) Longitudinal sections of the developing Eucalyptus?Pisolithus ectomycorrhiza synthesized in vitro (from Burgess et al., 1996 with permission). Fig. S3. Hierarchical clustering tree view of 395 symbiosis-regulated Pisolithus microcarpus and Eucalyptus globulus genes. Clustering analysis was carried out using the graph partitioning-based (GPB) paradigm in WCLUTO. Each horizontal line displays the expression ratio for one gene in symbiotic tissues vs free-living partners. The GPB clustering allowed to define subset of genes sharing similar expression profiles (clusters 0?6). Each gene is represented by a row of colored boxes and each stage is represented by a single column. Regulation levels range from pale to saturated colors (red for induction; green for repression). Black indicates no change in gene expression. Eucalyptus globulus genes are prefixed by ?Eg?. Fig. S4. Self-organizing map (SOM) clusters of expression profiles during Eucalyptus?Pisolithus ectomycorrhiza development. Each graph displays the mean pattern of expression of the transcripts in that cluster (blue lines) and the standard deviation of average expression (red lines). The number of transcripts (expressed sequence tags) in each cluster is at the top center of each SOM. The y-axis represents normalized gene expression levels. A list of genes in each cluster is also provided. Fig. S5. Reverse transcriptase-polymerase chain reaction (RT-PCR) expression patterns for representative Eucalyptus globulus and Pisolithus microcarpus SR-genes. Total RNA of free-living mycelium, nonmycorrhizal and mycorrhizal roots was isolated and aliquots of 1 ?g were used for first-strand cDNA synthesis. A PCR was performed with 2 ?l of first-strand cDNA and 20, 25, and 30 cycles. A control with no RT in the first strand cDNA synthesis reaction mix was included to control for the lack of genomic DNA. Eucalyptus- or Pisolithus-specific primers were used to amplify rDNA internal transcribed spacer sequence (ITS/5.8S rRNA) and to check for equal loading of plant or fungal RNA. Pm and Eg, P. microcarpus and E. globulus, respectively; M4, M7, M12, and M21 are 4-, 7-, 12-, and 21-d-old ectomycorrhiza, respectively.

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