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Fig. S1 GO terms associated with collinear genes.

Fig. S2 Relationship of secreted Colletotrichum subtilisins to plant subtilisins.

Fig. S3 Genomic region with auxin synthesis genes.

Fig. S4 Enriched GO terms in secretomes.

Fig. S5 Genomic region with Ave1.

Fig. S6 Quantitative PCR of selected small, secreted proteins.

nph12085-sup-0002-TableS1-S23.xlsxapplication/msexcel855K

Table S1 Homologs of genes required for repeat-induced point mutation

Table S2 Predicted genes on scaffolds with homology to the partial sequence of a C. gloeosporioides dispensible chromosome

Table S3 Proteases encoded in the C. orbiculare and C. gloeosporioides genomes according to MEROPS family

Table S4 CAZy family members associated with degradation of plant cell wall carbohydrates and chitin binding in C. orbiculare and C. gloeosporioide

Table S5 Nonenzymatic PFAM domains present in C. orbiculare secreted proteins but not in nonsecreted proteins

Table S6 Nonenzymatic PFAM domains present in C. gloeosporioides secreted proteins but not in nonsecreted proteins

Table S7 Number of selected nonenzymatic PFAM domains associated with infection in other phytopathogens as well as the ratio of predicted secreted proteins predicted to be carrying such domains relative to the rest of the genome

Table S8 List of C. orbiculare and Cgloeosporioides sequences in SSP tribes with three or more members

Table S9 Enriched GO terms associated with sequences upregulated in conidia 10-fold or more compared to in vitro-grown hyphae

Table S10 Enriched GO terms associated with sequences upregulated in 1 dpi 10-fold or more compared to in vitro-grown hyphae

Table S11 Enriched GO terms associated with sequences upregulated in 3 dpi 10-fold or more compared to in vitro-grown hyphae

Table S12 Enriched GO terms associated with sequences upregulated in 7 dpi 10-fold or more compared to in vitro-grown hyphae

Table S13 Top 100 most highly expressed genes at 1 dpi

Table S14 Top 100 most highly expressed genes at 3 dpi

Table S15 Top 100 most highly expressed genes at 7 dpi

Table S16 Top 100 most highly expressed genes in conidia

Table S17 Most highly expressed genes in in vitro-grown hyphae

Table S18 Expression of homologs of known effectors from other fungi with differential expression in planta compared to in vitro-grown hyphae

Table S19 Expression values of major facilitator superfamily (MFS) transporters

Table S20 Secondary metabolite clusters predicted in Corbiculare by SMURF

Table S21 Secondary metabolite clusters predicted in Cgloeosporioides by SMURF

Table S22 Conservation of C. orbiculare secondary metabolite cluster genes in Cgloeosporioides, C. higginsianum and C. graminicola

Table S23 Conservation of C. gloeosporioides secondary metabolite cluster genes in Corbiculare, C. higginsianum and C. graminicola