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Nat Microbiol. 2018 Dec;3(12):1417-1428. doi: 10.1038/s41564-018-0261-0. Epub 2018 Oct 8.

Leveraging single-cell genomics to expand the fungal tree of life.

Author information

1
US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
2
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
3
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
4
Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA.
5
Ottawa Hospital Research Institute, Centre for Innovative Cancer Research, Ottawa, Ontario, Canada.
6
Architecture et Fonction des Macromolécules Biologiques, UMR 7857 CNRS, Aix-Marseille University, Marseille, France.
7
Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.
8
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
9
Department of Plant Pathology, University of Florida, Gainesville, FL, USA.
10
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA. tyjames@umich.edu.
11
US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. ivgrigoriev@lbl.gov.
12
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA. ivgrigoriev@lbl.gov.

Abstract

Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.

PMID:
30297742
DOI:
10.1038/s41564-018-0261-0

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