Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes

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DOI

https://doi.org/10.1093/gbe/evab047

Language of the publication
English
Date
2021-03-09
Type
Article
Author(s)
  • Tagirdzhanova, Gulnara
  • Saary, Paul
  • Tingley, Jeffrey P.
  • Díaz-Escandón, David
  • Abbott, D. Wade
  • Finn, Robert D.
  • Spribille, Toby
Publisher
Oxford University Press

Abstract

Basidiomycete yeasts have recently been reported as stably associated secondary fungal symbionts 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 secondary fungal symbionts 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 harbors the majority of predicted secondary metabolite clusters. The basidiomycete genomes possess ∼35% fewer predicted genes than the ascomycete and have reduced secretomes even compared with 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.

Subject

  • Agriculture

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Peer review

Yes

Open access level

Gold

Article

Journal title
Genome Biology and Evolution
Journal volume
13
Journal issue
4
Article number
evab047
Accepted date
2021-03-03

Citation(s)

Tagirdzhanova, G., Saary, P., Tingley, J. P., Díaz-Escandón, D., Abbott, D. W., Finn, R. D., & Spribille, T. (2021). Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes. Genome Biology and Evolution, 13(4), Article evab047. https://doi.org/10.1093/gbe/evab047

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Biology

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