Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti

Fig. S1. A cladogram representation of the phylogenetic relations between the species in this paper. The red labels show bootstrap values of 100 % and the black labels show bootstrap values < 100 %. <br />Fig. S2. Phylogenetic relation and InterPro coverage of the fungal species included in this study. A. Dendrogram of the phylogenetic relation between the 32 species. The black boxes represent the homologous proteins among the species branching from the nodes. The white boxes represent the proteins unique to the specific species. B. Proteome sizes of each species (gray). C. Core proteome size of each species (red). D. Species unique proteins (yellow). The dark colored boxes represent proteins with InterPro annotation, the light-colored boxes represent the proteins with no annotation. The numbers at right side of the boxes indicates the total number of annotated and not annotated genes. The bar scales are unique to each graph. <br />Fig. S3. Phylogenetic relation and InterPro coverage of all Aspergilli. A. Dendrogram of the phylogenetic relation between the 29 Aspergillus species. The black boxes represent the homologous proteins among the species branching from the nodes. The white boxes represent the proteins unique to the specific species. B. Proteome sizes of each species (gray). C. Core proteome size of each species (red). D. Species unique proteins (yellow). The dark colored boxes represent proteins with InterPro annotation, the light-colored boxes represent the proteins with no annotation. The numbers at right side of the boxes indicates the total number of annotated and not annotated genes. The bar scales are unique to each graph. <br />Fig. S4. Phylogenetic relation and InterPro coverage of the species in section Usti. A. Dendrogram of the phylogenetic relation between the 13 species. The black boxes represent the homologous proteins among the species branching from the nodes. The white boxes represent the proteins unique to the specific species. B. Proteome sizes of each species (gray). C. Core proteome size of each species (red). D. Species unique proteins (yellow). The dark colored boxes represent proteins with InterPro annotation, the light-colored boxes represent the proteins with no annotation. The numbers at right side of the boxes indicates the total number of annotated and not annotated genes. The bar scales are unique to each graph. <br />Fig. S5. Growth profile of the different species using a wide range of plant biomass related substrates. A. granulosus did not grow on any media, so this one is not present in the picture. <br />Fig. S6. The collected number of CAZy families per species group. A histogram representation of the number of proteins within each CAZy class for each CAZy family. The species groups are indicated by color. CAZy class; auxiliary activities (AA), carbohydrate-binding molecules (CBM), carbohydrate esterases (CE), polysaccharide lyases (PL), distant plant expansins (EXPN), glycosyltransferases (GT), and glycoside hydrolases (GH). <br />Fig. S7. The number of CAZy families in relation to species group proteome size (percentage). A histogram representation of the percentage of proteins within each CAZy class for each CAZy family. The species groups are indicated by color. CAZy class; auxiliary activities (AA), carbohydrate- binding molecules (CBM), carbohydrate esterases (CE), polysaccharide lyases (PL), distant plant expansins (EXPN), glycosyltransferases (GT), and glycoside hydrolases (GH). <br />Fig. S8. Synteny plot of a NRPS-like secondary metabolite gene cluster family shared by species from section Usti, section Nidulantes, section Cavernicolus and section Ochraceorosei. Annotated InterPro domains. A. NRPS-like. B. General substrate transporter. C. Carboxylesterase, type B. D. BTB/POZ. E. NAD-dependent epimerase/dehydratase. H. NmrA-like domain. I. Transcription factor domain. J. Alpha/beta hydrolase fold-1. K. Domain of unknown function. L. Glucose-methanol-choline oxidoreductase. M. Major facilitator superfamily. N. Male sterility. O. Short- chain dehydrogenase/reductase SDR. P. Transferase. Q. WD40 repeat. R. Zinc/iron permease. S. Zn(2)-C6 fungal-type DNA-binding domain. T. Transcription factor domain. NA: no annotation. <br />Fig. S9. Percentage shared secondary metabolite gene clusters between the 29 Aspergillus species and Penicillium chrysogenum. The heatmap has been clustered based on the number of shared secondary metabolites on both axis. <br />Fig. S10. Synteny plot of a NRPS-like secondary metabolite gene cluster family shared by all species from section Usti except for A. lucknowensis. Annotated InterPro domains. A. Cytochrome P450. B. NAD-dependent epimerase/dehydratase. C. PKS. D. Major facilitator superfamily. E. NRPS- Like. H. Oxoglutarate/iron-dependent dioxygenase. I. O-methyltransferase, family 2. J. FAD linked oxidase. K. FAD linked oxidase. L. GNAT domain. M. Rad1/Rec1/Rad17. N. SANT/Myb domain. O. General substrate transporter. P. Heavy metal-associated domain. Q. ABC transporter-like. R. Alpha/beta hydrolase fold-1. S. Alpha/beta hydrolase fold-5. T. Ankyrin repeat-containing domain. U. Cell wall galactomannoprotein. V. Cytochrome P450. W. Domain of unknown function. X. Translation elongation factor EF1B. Y. Fatty acid desaturase, type 1. Z. Fatty acid hydroxylase. AA. General substrate transporter. AB. Glutathione S-transferase. AC. Glycoside hydrolase. AD. Glycosyltransferase family 28. AE. Male sterility, NAD-binding. AF. Mitochondrial substrate/solute carrier. AG. MmgE/PrpD. AH. NmrA-like domain. AI. Protein kinase domain. AJ. Pyridine nucleotide- disulphide oxidoreductase. AK. Taurine catabolism dioxygenase TauD/ TfdA. AL. Transcription factor domain. AM. Transcription factor domain, fungi. NA: no annotation. <br />Table S1. Sequencing and annotation statistics of the investigated species. <br />Table S2.1. The InterPro domains for the core proteome of genus Aspergillus. The InterPro domains found in Vesth et al. (2018) is marked by x. <br />Table S2.2. The InterPro domains for the species-unique proteins of genus Aspergillus. The InterPro domains found in Vesth et al. (2018) is marked by x. <br />Table S3. Identification of unique InterPro domains per section. <br />Table S3.1. The InterPro domains of the proteins unique to all species in section Usti. <br />Table S3.2. The InterPro domains of the proteins unique to all species in section Cavernicolus. <br />Table S4. Proteins with predicted CAZy families and definitions of all species in this study. <br />Table S5. Comparison of CAZy genome content. <br />Table S5.1. Total numbers of Glycoside Hydrolases (GH), Glycosyl Transferases (GT), Polysaccharide Lyases (PL), Carbohydrate Esterases (CE), Carbohydrate Binding Modules (CBM) and Auxiliary Activities (AA). <br />Table S5.2. Detailed comparison of Glycoside Hydrolases (GH). <br />Table S5.3. Detailed comparison of Glycosyl Transferases (GT). <br />Table S5.4. Detailed comparison of Polysaccharide Lyases (PL). <br />Table S5.5. Detailed comparison of Carbohydrate Esterases (CE). <br />Table S5.6. Detailed comparison of Carbohydrate Binding Modules (CBM). <br />Table S5.7. Detailed comparison of Auxiliary Activities (AA). <br />Table S5.8. Cellulose-related families. <br />Table S5.9. Xylan-related families. <br />Table S5.10. Mannan-related families. <br />Table S5.11. Xyloglucan-related families. <br />Table S5.12. Pectin-related families. <br />Table S5.13. Starch-related families. <br />Table S5.14. Inulin-related family GH32. <br />Table S5.15. Comparison of CAZymes related to plant biomass degradation. <br />Table S6. The predicted secondary metabolite gene clusters and their InterPro annotations and MIBiG associated compounds.