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

Steven Ahrendt (1) , C Alisha Quandt (2, 3) , Doina Ciobanu (4) , Alicia Clum (5) , Asaf Salamov (6) , Bill Andreopoulos (7) , Jan-Fang Cheng (5) , Tanja Woyke (5) , Adrian Pelin (8) , Bernard Henrissat (9) , Nicole Reynolds (8) , Gerald Benny (10) , Matthew Smith (10) , Timothy James (2) , Igor Grigoriev (5)

1 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
2 University of Michigan [Ann Arbor]
3 OSU - Oregon State University
4 DOE Joint Genome Institute [Walnut Creek]
5 DOE - Department of Energy / Joint Genome Institute
6 United States Department of Energy
7 BIOTEC - Biotechnology Center [Dresden]
8 OHRI - Ottawa Hospital Research Institute [Ottawa]
9 AFMB - Architecture et fonction des macromolécules biologiques
10 UF - University of Florida [Gainesville]

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.

Keywords: multiple sequence alignment; phylogeny; gene; classification; annotation; discovery; zoopagomycotina; superfamily

Keywords: syncephalis zoopagales; evolution

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]

Steven Ahrendt, C Alisha Quandt, Doina Ciobanu, Alicia Clum, Asaf Salamov, et al.. Leveraging single-cell genomics to expand the fungal tree of life. Nature Microbiology, 2018, 3 (12), pp.1417-1428. ⟨10.1038/s41564-018-0261-0⟩. ⟨hal-02094482⟩