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

Steven R Ahrendt,Igor V Grigoriev,Adrian Pelin,Nicole K Reynolds,Asaf Salamov,Timothy Y James,Matthew E Smith,Alicia Clum,Tanja Woyke,Bernard Henrissat,Jan-Fang Cheng,Doina Ciobanu,Bill Andreopoulos,C Alisha Quandt,Gerald L Benny

doi:10.1038/s41564-018-0261-0

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.

Highlights

Environmental DNA surveys reveal that most fungal diversity represents uncultured species
Despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs
CEGMA percentages increased when more cells were incorporated into a library, ranging from 2.8% (1 cell, C. protostelioides) to 96.7% (100 cell, M. bicuspidata)

Summary

Introduction

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. Much of what we know about the evolution of the fungal metabolic repertoire is biased towards fungi that are model systems, enzyme factories or important human or plant pathogens[2] This emphasis results in an underrepresentation of uncultured lineages in the fungal genomic tree and the inaccessibility of these clades to comparative genomic analysis. Most studies recover species that are not represented in genomic databases[3,4,5] This demonstrates a collectively limited knowledge of the true diversity of fungi, a problem exacerbated when considering early-diverging lineages, which are primarily microscopic and diverse in biotrophic groups[1,6].

Methods

Results

Conclusion