The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Genomics, Microbiology, Mycology
- Keywords
- Microbiome, Microbial communities, Symbiosis, Biotic interactions, Comparative genomics, Fungal evolution
- Copyright
- © 2017 Bahram et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. PeerJ Preprints 5:e3408v3 https://doi.org/10.7287/peerj.preprints.3408v3
Abstract
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.
Author Comment
This is replaces the previous version in which an old version had been uploaded in error.
Supplemental Information
Table S1
Table S1. Major features of the genome of Inocybe terrigena.
Table S4
Table S4. Features and taxonomic identification of contigs assembled based on Inocybe terrigena metagenome.
Table S2
Table S2. Genes identified from fungal contigs based on Inocybe terrigena metagenome. Tabs present basic features, KEGG id and KEGG pathways retrieved from GhostKOALA.
Table S4
Table S4. Features and taxonomic identification of contigs assembled based on Inocybe terrigena metagenome.
Table S5
Table S5. Genomes used for comparative genomics.
Table 6
Table S6. CAZyme gene profiles of 59 Agaricomycetes genomes used in comparative genomics analysis.
Perl pipeline
Perl pipeline used for metagenomic analysis.
Figure S1
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 S2
Figure S2. The relative abundance of fungal functional gene categories in Inocybe terrigena genome.
Figure S3
Figure S3. Relationship of contig coverage and contig length of dominant bacterial genera in I. terrigena.
Figure 4
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.