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emi12080-sup-0001-fS1.tif1750K

Fig. S1. RNA isolation, amplification and cDNA synthesis obtained from Tuber melanosporum/Corylus avellana microdissected tissues.

A. Electrophoretic profiles of total RNA.

B. Derived amplified RNA (aRNA).

C. cDNA isolated from mantle (M), Hartig net (HN) and vascular cells (VC) of T. melanosporum/C. avellana ectomycorrhiza.

D. Concentrations of total RNA, aRNA and cDNA used for microarrays experiment are presented.

emi12080-sup-0002-fS2.tif1579K

Fig. S2. Principal component analysis (PCA) of Tuber melanosporum transcript.

A. PCA of T. melanosporum transcript levels measured for the microdissected samples. Three biological replicates for mantle (M), Hartig net (HN) and one for vascular cells (VC) were used for the PCA and the correlation circle is presented. Expression level of each gene assessed in a given biological situation and biological replicate was reported to the mean expression level calculated for the seven hybridizations and was log10-normalized before proceeding with PCA. The PCA plot places biological conditions along the two axes (components 1 and 2) explaining 29.22% and 19.94% of the variance observed within samples.

B. PCA of T. melanosporum transcript levels measured for the microdissected samples and the three fungal developmental stages. In addition to the samples described in A, seven biological replicates for free-living mycelium (FLM), five for truffle (FB) and four for ectomycorrhizal roots tips (ECM) were included. The PCA plot places biological conditions along the two axes explaining 22.62% and 12.67% of the variance observed within samples.

emi12080-sup-0003-fS3.tif2801K

Fig. S3. Mapping of gene expression levels onto nitrogen-related metabolism pathways. Gene expression levels measured in Tuber melanosporum mantle and Hartig net were mapped onto three KEGG pathways related to alanine, aspartate and glutamate metabolism, arginine and proline metabolism and nitrogen metabolism. Each box corresponds to a specific enzyme. Gene expression levels measured in the fungal mantle and in the Hartig net are depicted in red (pale red: low expression levels; dark red: high expression levels). White boxes correspond to enzymes that were not identified in T. melanosporum genome. Genes significantly regulated between the two compartments are highlighted in green (P < 0.05, PPDE > 0.97, fold change > 2.5).

emi12080-sup-0004-fS4.tif2517K

Fig. S4. Mapping of gene expression levels onto carbon-related metabolism pathways. Gene expression levels measured in Tuber melanosporum mantle and Hartig net were mapped onto three KEGG pathways related to glycolysis/gluconeogenesis, citrate cycle and pentose phosphate pathway. Gene expression levels measured in the fungal mantle and in the Hartig net are depicted in red (pale red: low expression levels; dark red: high expression levels). White boxes correspond to enzymes that were not identified in T. melanosporum genome. Genes significantly regulated between the two compartments are highlighted in green (P < 0.05, PPDE > 0.97, fold change > 2.5).

emi12080-sup-0005-tS1.xls132K

Table S1. (Excel file) List of Tuber melanosporum genes significantly upregulated in the fungal mantle versus the Hartig net (fold change > 2.5; P < 0.05 and PPDE > 0.97) and ranked according to their expression ratios.

emi12080-sup-0006-tS2.xls143K

Table S2. (Excel file) List of Tuber melanosporum genes significantly upregulated in the Hartig net versus the fungal mantle (fold change > 2.5; P < 0.05 and PPDE > 0.97) and ranked according to their expression ratios.

emi12080-sup-0007-tS3.xls66K

Table S3. (Excel file) List of the 100 most highly expressed Tuber melanosporum genes in the fungal mantle.

emi12080-sup-0008-tS4.xls47K

Table S4. (Excel file) List of the 100 most highly expressed Tuber melanosporum genes in the Hartig net.

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