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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biodiversity
  • DNA, Ribosomal / genetics
  • Fungi / classification
  • Fungi / enzymology
  • Fungi / genetics*
  • Fungi / metabolism*
  • Genetic Variation
  • Genome, Fungal*
  • Genomics*
  • Heterozygote
  • Life Cycle Stages
  • Metabolic Networks and Pathways / genetics
  • Metabolic Networks and Pathways / physiology
  • Phylogeny
  • Polymorphism, Genetic
  • RNA, Ribosomal, 18S / genetics
  • Secondary Metabolism / genetics
  • Secondary Metabolism / physiology
  • Sequence Analysis, DNA
  • Symbiosis / genetics
  • Symbiosis / physiology


  • DNA, Ribosomal
  • RNA, Ribosomal, 18S