Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome
Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate-active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.
Fig. S1. Workflow. Graphical representation of the workflow for obtaining the contigs of the target genome, E. granulatus.
Fig. S2. Mitochondrial genome alignment. Progressive Mauve alignment of mitochondrial genome assemblies of E. granulatus and Aspergillus fumigatus. Coloured blocks represent homologous sequence free of rearrangements, and height within blocks correspond to sequence conservation.
Fig. S3. Adenylation domain phylogeny. Red box encloses the Adenylation domains specific to an E. granulatus NRPS that are part of a species-specific lineage expansion. Species abbreviations are as follows: Aspfu, Aspergillus fumigatus; Anid, Aspergillus nidulans; B_bassiana, Beauveria bassiana; Ch, Cochliobolus heterostrophus; Cp, Claviceps purpurea; Ef, Epichloë festucae; Egran, E. granulatus; Fe, Fusarium equiseti; Fh, Fusarium heterosporum; Hv, Trichoderma virens; Lm, Leptosphaeria maculans; Ma/MAA, Metarhizium anisopliae; Mg, Magnaporthe grisea; Pench, Penicillium chrysogenum; Talstip, Talaromyces stipitatus; TOPH, Tolypocladium ophioglossoides (parasite of Elaphomyces spp.).
Fig. S4. Species richness rarefaction. Rarefaction curves for species richness versus sampling depth for the two peridium libraries with paired-end reads uploaded separately (2 reads per library). MG-RAST IDs are given to the right of the curves.
Fig. S5. Taxonomy Pie Chart. Percentages of the microbiome reads in the E. granulatus peridium annotated at the domain level.
Fig. S6. Rarefaction of ECs. Rarefaction of the enzyme commission numbers for E. granulatus peridium microbiome with subsample size of 250.
Fig. S7. KEGG Map. KeggMapper visualization of the Enzyme Categories present in the E. granulatus peridium annotated by MG-RAST (highlighted in purple).
Table S1. List of 35 bacteria. List of the 35 bacterial genomes used in the bacterial database to removed raw reads using Bowtie 2.
Table S2. Genome assembly statistics for Caliciopsis orientalis and Monascus ruber, both of which are being published for the first time here. *Sequenced and assembled at Oregon State University using methods described in text. **Sequenced and assembled at the Joint Genomes Institute as a part of 1KFG CSP. ***Ab initio models created in AUGUSTUS – no RNA sequenced.
Table S3. Table of CAZymes. Counts of CAZymes for the selected Eurotiomycetes and Pezizomycetes analysed in this study, including E. granulatus (highlighted in yellow), other Eurotiales (green), Onygenales (pink), Caliciopsis orientalis (olive) and Pezizales (blue). Species abbreviations as in Fig. 3. CAZyme class/module abbreviations: auxiliary activities (AA), carbohydrate-binding module (CBM), carbohydrate esterase (CE), glycoside hydrolase (GH), glycosyltransferase (GT), polysaccharide Lyase (PL).
Table S4. Overrepresented clusters in E. granulatus. MCL clusters, generated through the Hal pipeline at 1.2 inflation parameter, in which E. granulatus is overrepresented compared with species in Fig. 2. To conserve space, non- Eurotiomycetes have been removed, except for Tuber melanosporum (Tum). The average number of protein models per cluster per taxon for all taxa in Fig. 2 is presented in the last column. Putative annotations are given, where known. Species abbreviations as in Fig. 3.
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