The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics

• Published in: PeerJ preprints 2017-11
• Main Authors: Mohammad Bahram, Vanderpool, Dan, Pent, Mari, Hiltunen, Markus, Ryberg, Martin
• Format: Article
• Language: English
• Subjects: Bacteria; Biodegradation; Brown rot; Ectomycorrhizas; Fruit bodies; Fungi; Genomes; Lignin; Symbiosis; White rot
• ISSN: 2167-9843
• DOI: 10.7287/peerj.preprints.3408v1

Although recent advances in molecular methods have facilitated understanding the evolution of fungal symbiosis, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Basidiomycota), a largely uncultured ectomycorrhizal clade that form symbiotic associations with a wide variety of plant species. Using metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, followed by classifying contigs into fungi and bacteria based on BLAST alignments as well as their differential coverage and GC content, we obtained a highly complete fungal genome, containing 93% of core eukaryotic genes. I. terrigena genome was more related to previously published ectmycorrhizal and brown rot than white rot genomes; however, it showed a significant reduction in lignin degradation capacity compared to closely related ectomycorrhizal clades, supporting independent evolution of ectomycorrhizal symbiosis in Inocybe. The microbiome of I. terrigena harboured bacteria with relatively high-coverage assemblies as well as with known symbiotic functions in hypogeous fungal tissues, suggesting the symbiotic functions of these bacteria in fungal tissues independent of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.