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Bahram M, Vanderpool D, Pent M, Hiltunen M, Ryberg M.2017. The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. PeerJ Preprints5:e3408v3https://doi.org/10.7287/peerj.preprints.3408v3
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.
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Table S1. Major features of the genome of Inocybe terrigena.
Figure S1. The I. terrigena genome includes a smaller number of genes compared to other ecotmycorrhizal genomes. Boxplot showing the number of gene models reported previously for different functional guilds of fungi. Dash line corresponds to the number of gene models uncovered for Inocybe terrigena in this study.
Figure 4. Pie chart showing the relative abundance of bacterial gene functional categories in Inocybe terrigena fruitbody based on KEGG Orthology groups (A) and Subsystems (B). Functional categories with relative abundance of ≥ 0.5% are presented. Only contigs that were initially identified as bacteria based on BLAST searches were included.