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Fig. S1 The diversity and distribution of class I and class II transposable elements in Heterobasidion irregulare.

Fig. S2 Genomic landscape of Heterobasidion irregulare.

Fig. S3 Estimated time since the major long terminal repeat (LTR) retrotransposon activity in the Heterobasidion irregulare genome.

Fig. S4 Frequency of simple sequence repeats (SSRs) in selected genome fractions of Heterobasidion irregulare.

Fig. S5 Transcription factor (TF) family distribution across fungal taxa.

Fig. S6 Ste50 proteins from basidiomycota and ascomycota.

Fig. S7 Phylogenetic analysis of the adenylatecyclase proteins from basidiomycota, ascomycota and oomycota.

Fig. S8 Comparative map of gene order surrounding the MAT-A locus in representative Agaricomycetes.

Fig. S9 Cosegregation of the MAT-A region (MIP) and mating type among a progeny array of Heterobasidion irregulare.

Fig. S10 Phylogenetic analysis of class II peroxidases from various fungal taxa.

Fig. S11 Unrooted phylogram of Cerato-platanin (Cp) protein family including the three Heterobasidion irregulare proteins.

Table S1 Genomic libraries included in the Heterobasidion irregulare genome assembly and their respective assembled sequence coverage levels in the whole-genome shotgun assembly

Table S2 Summary statistics of the draft whole-genome shotgun assembly of Heterobasidion irregulare before screening and removal of organelles and contaminating scaffolds

Table S3 Predicted gene models in Heterobasidion irregulare and supporting lines of evidence

Table S4 Characteristics of predicted gene models in Heterobasidion irregulare

Table S5 Number of orthologs between Heterobasidion irregulare and six other basidiomycetes

Table S6 Functional annotation of Heterobasidion irregulare proteins

Table S7 Top 30 PFAM domains in Heterobasidion irregulare proteome

Table S8 Statistics of the Heterobasidion irregulare assembly

Table S9 Total length (bp per megabase of DNA) of fully standardized di- and trinucleotide repeats in different genomic regions of the Heterobasidion irregulare genome and of other fungal genomes

Table S10 Protein-coding genes, rRNA genes and introns in the mitochondrial genome of Heterobasidion irregulare

Table S11 Distribution of reactive oxygen species (ROS)-related proteins among various fungal species

Table S12 Comparison of numbers of genes putatively involved in lignin degradation in the genomes of several wood-degrading basidiomycete fungi

Table S13 Distribution of genes coding for membrane transporter families in Heterobasidion irregulare, and comparison with other sequenced basidiomycetes

Table S14 Distribution of genes coding for proteinase families in Heterobasidion irregulare, and comparison with other sequenced basidiomycetes

Table S15 Distribution of proteinase family members in Heterobasidion irregulare

Table S16 Summary of glycoside hydrolases, polysaccharide lyases and carbohydrate esterases genes in Heterobasidion irregulare

Table S17 Carbohydrate-active enzymes of Heterobasidion irregulare active on plant cell walls

Table S18 Gene models up-regulated >10 fold during Heterobasidion irregulare growth on wood

Table S19 Location and characteristics of gene models putatively involved in lignin degradation in the Heterobasidion irregulare genome

Table S20 Annotated putative natural product genes in the Heterobasidion irregulare genome

Table S21 Putative natural product gene clusters in the Heterobasidion irregulare genome

Table S22 The 250 gene models with the highest expression during Heterobasidion irregulare growth in the cambial zone of necrotic bark tissue

Table S23 Gene models up-regulated during Heterobasidion irregulare growth in cambial zone of necrotic bark tissue

Table S24 Number of carbohydrate-active enzymes significantly up-regulated during Heterobasidion irregulare growth in wood and in the cambial zone of necrotic bark tissue

Table S25 Number of transporters significantly up-regulated during Heterobasidion irregulare growth in wood and in cambial zone of necrotic bark tissue

Notes S1 Simple sequence repeats and transposable elements.

Notes S2 The mitochondrial genome annotation and analysis.

Notes S3 Targeted annotation of specific gene families.

Notes S4 The mating incompatibility locus (MAT).

Notes S5 Wood degradation, enzyme content, expression and growth.

Notes S6 Pathogenicity.

Notes S7 Trade-off.

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NPH_4128_sm_FigS1-S11.docx1996KSupporting info item
NPH_4128_sm_NotesS1-S7.doc166KSupporting info item
NPH_4128_sm_TableS1-S25.docx130KSupporting info item