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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 University of Florida [Gainesville]
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.
Keywords : multiple sequence alignment phylogeny gene classification annotation discovery zoopagomycotina superfamily
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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, Nature Publishing Group, 2018, 3 (12), pp.1417-1428. ⟨10.1038/s41564-018-0261-0⟩. ⟨hal-02094482⟩

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