DOI: 10.5061/dryad.c2fqz617h
title: Data from: Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes

description: Basidiomycete yeasts have recently been reported as stably associated
 secondary fungal symbionts (SFSs) of many lichens, but their role in the
 symbiosis remains unknown. Attempts to sequence their genomes have been
 hampered both by the inability to culture them and their low abundance in
 the lichen thallus alongside two dominant eukaryotes (an ascomycete fungus
 and chlorophyte alga). Using the lichen Alectoria sarmentosa, we
 selectively dissolved the cortex layer in which SFSs are embedded to
 enrich yeast cell abundance and sequenced DNA from the resulting slurries
 as well as bulk lichen thallus. In addition to yielding a near-complete
 genome of the filamentous ascomycete using both methods, metagenomes from
 cortex slurries yielded a 36- to 84-fold increase in coverage and
 near-complete genomes for two basidiomycete species, members of the
 classes Cystobasidiomycetes and Tremellomycetes. The ascomycete possesses
 the largest gene repertoire of the three. It is enriched in proteases
 often associated with pathogenicity and harbours the majority of predicted
 secondary metabolite clusters. The basidiomycete genomes possess ∼35%
 fewer predicted genes than the ascomycete and have reduced secretomes even
 compared to close relatives, while exhibiting signs of nutrient limitation
 and scavenging. Furthermore, both basidiomycetes are enriched in genes
 coding for enzymes producing secreted acidic polysaccharides, representing
 a potential contribution to the shared extracellular matrix. All three
 fungi retain genes involved in dimorphic switching, despite the ascomycete
 not being known to possess a yeast stage. The basidiomycete genomes are an
 important new resource for exploration of lifestyle and function in
 fungal-fungal interactions in lichen symbioses.
description: <strong>Acidobacteria_rpob.fa</strong><br>
 Nucleotide sequences of rpoB of Acidobaceria produced during this study
 and used for phylogeny
 <strong>Cyphobasidiales_its.fa</strong><br>
 Nucleotide sequences of Cyphobasidiales ITS produced during this study and
 used for phylogeny
 <strong>Tremellales_its.fa</strong><br>
 Nucleotide sequences of Tremellales ITS produced during this study and
 used for phylogeny
 <strong>Alectoria.annotations.txt</strong><br>
 Full annotation table produced by funannotate for the lecanoromycete
 MAG
 <strong>Cyphobasidium.annotations.txt</strong><br> Full annotation table produced by funannotate for the Cyphobasidium MAG <strong>Tremella.annotations.txt</strong><br> Full annotation table produced by funannotate for the Tremella MAG <br> <strong>coverage.sh</strong><br> Script producing coverage files (used to make GC-coverage plots) from the metagenomic assemblies and fastq files <strong>gc-coverage-plot.R</strong><br> R script used to make the GC-coverage plots <strong>funannotate_annotation.sh</strong><br> Wrapper script used to produce genome annotations using the funannotate pipeline <strong>get_secretome.R</strong> <br> R scrip used to combine annotations produced by SignalP, TMHMM, and WolfPSORT to produce secretome fasta files.