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

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.

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

“…Sequence information on zoosporic fungi is currently very limited, which poses challenges to obtaining a robust chytrid tree of life. This situation fortunately is changing, and thanks to the application of single‐cell‐based techniques genomic and environmental sampling is steadily increasing (Grossart et al ., ; Ahrendt et al ., ).…”

“…While their small size imposes challenges to traditional sequencing approaches, they are prime candidates for single‐cell sequencing‐based techniques. Using the latter methods, several genomes in these lineages have been sequenced recently (Ahrendt et al ., ).…”

“…The evolutionary relationships among the different families are not well resolved, mostly due to the difficulty of working with such small and usually unculturable fungi (Davis et al ., ). Additionally, molecular analyses suggest that members of this clade show high evolutionary rates (Ahrendt et al ., ; Davis et al ., ), and some of the most commonly used primers for barcode sequences of fungi or eukaryotes work poorly for this group (Tedersoo & Lindahl, ). This amplification problem is caused by their unusually long internal transcribed spacer (ITS) sequences, so the recent development of more‐specific primers (Lazarus et al ., ) will help the study of these fungi to catch up with the rest of the kingdom.…”

Systematic review of publicly available non-Dikarya fungal proteomes for understanding their plant biomass-degrading and bioremediation potentials

“…Microsporidia (Antonospora locustae HM-2013 (Slamovits et al 2004), Encephalitozoon cuniculi GB-M1 (Peyretaillade et al 2009), Encephalitozoon hellem ATCC 50504 (Pombert et al 2012), Encephalitozoon intestinalis ATCC 50506 (Corradi et al 2010), Encephalitozoon romaleae SJ-2008 (Pombert et al 2012), Enterocytozoon bieneusi H348 (Akiyoshi et al 2009), Nematocida parisii ERTm1 (Cuomo et al 2012), Nosema ceranae BRL01 ). Cryptomycota (Rozella allomycis CSF55 (James et al 2013), Rozella allomycis CSF55 single-cell v1.0 (Ahrendt et al 2018). We have also reported a tentative average of cellulolytic, hemicellulolytic, ligninolytic and pectinolytic potentials exhibited by the fungi belonging to the selected phyla, by considering the total number of genes encoding for the lignocellulolytic enzymes.…”

“…Jimgerdemannia lactiflua OSC166217 (Chang et al 2019). Zoopagomycotina Piptocephalis cylindrospora RSA 2659 single-cell v3.0 (Ahrendt et al 2018), Syncephalis pseudoplumigaleata Benny S71-1 single-cell v1.0 (Ahrendt et al 2018), Thamnocephalis sphaerospora RSA 1356 single-cell v1.0 (Ahrendt et al 2018). Entomophthoromycotina (Conidiobolus coronatus NRRL28638 v1.0 (Chang et al 2015).…”