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

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RT @SystBio_UU: Check the #Preprint #SystBioPaper Bahram et al "The genome and microbiome of a dikaryotic fungus (#Inocybe terrigena) revea…
Check the #Preprint #SystBioPaper Bahram et al "The genome and microbiome of a dikaryotic fungus (#Inocybe terrigena) revealed by #metagenomics"!
The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics https://t.co/LU5AvUuMRn #microbiomebot
The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics https://t.co/8Hc9OwUDy8
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The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics https://t.co/c5knsUUbni
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Supplemental Information

Table S1

Table S1. Major features of the genome of Inocybe terrigena.

DOI: 10.7287/peerj.preprints.3408v1/supp-1

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.

DOI: 10.7287/peerj.preprints.3408v1/supp-2

Table S3

Table S3. Results of CEGMA (Statistics of the completeness of the genome based on 248 CEGs).

DOI: 10.7287/peerj.preprints.3408v1/supp-3

Table S4

Table S4. Features and taxonomic identification of contigs assembled based on Inocybe terrigena metagenome.

DOI: 10.7287/peerj.preprints.3408v1/supp-4

Table S5

Table S5. Genomes used for comparative genomics.

DOI: 10.7287/peerj.preprints.3408v1/supp-5

Perl pipeline

Perl pipeline used for metagenomic analysis.

DOI: 10.7287/peerj.preprints.3408v1/supp-6

Astral tree

ASTRAL phylogeny.

DOI: 10.7287/peerj.preprints.3408v1/supp-7

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.

DOI: 10.7287/peerj.preprints.3408v1/supp-8

Figure S2

Figure S2. The relative abundance of fungal functional gene categories in Inocybe terrigena genome.

DOI: 10.7287/peerj.preprints.3408v1/supp-9

Figure S3

Figure S3. Relationship of contig coverage and contig length of dominant bacterial genera in I. terrigena.

DOI: 10.7287/peerj.preprints.3408v1/supp-10

Additional Information

Competing Interests

The authors declare no conflict of interest.

Author Contributions

Mohammad Bahram conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Dan Vanderpool performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Mari Pent performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Markus Hiltunen performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Martin Ryberg conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Raw Illumina reads are available at the Sequence Read Archive (SRA) under accession number SRP066410.

Data Deposition

The following information was supplied regarding data availability:

We have uploaded the codes as supporting information along with the manuscript.

Funding

The authors received support from Science for Life Laboratory, the National Genomics Infrastructure, NGI, and Uppmax provided assistance in massive parallel sequencing and computational infrastructure. Funding was provided by Uppsala University (Department of Organismal Biology) and Kaptain Carl Stenholm. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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