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Fig. S1 Strategy for removing reads from oak-interacting organisms.

Fig. S2 Representation of reads with homology to Arabidopsis accessions in 16 pedunculate oak Roche 454 transcript libraries.

Fig. S3 Comparison of the oak assemblies generated by the MIRA and Trinity assembly programs with reference databases.

Fig. S4 Relatedness of the contigs in the OakContigDF159.1 reference transcriptome to sequences in the GenBank nr database.

Fig. S5 Classification of contigs in the OakContigDF159.1 reference transcriptome by Gene Ontology terms.

Fig. S6 Comparison of coverage of global KEGG metabolic pathways by the OakContigDF159.1 reference transcriptome relative to the Arabidopsis thaliana proteome.

Fig. S7 Mycorrhiza formation on oak roots leads to increased transcript abundances of contigs associated with starch metabolism in comparison with the abundance in fine roots.

Table S1 Quantitative polymerase chain reaction primers

Table S2 Numbers and lengths of oak transcripts obtained by Roche 454 sequencing

Table S3 Transcripts in roots and leaves of oak DF159 microcuttings and in EMs synthesized with Piloderma croceum as revealed by Illumina sequencing

Table S4 GO annotation of contigs in the OakContigDF159.1 reference transcriptome

Table S5 GO enrichment analysis of EMs synthesized between pedunculate oak DF159 microcuttings and Piloderma croceum

Table S6 Differentially expressed transcripts in EMs synthesized between microcuttings of the pedunculate oak clone DF159 and Piloderma croceum

Methods S1 Supporting methods.