Recovering genomes from uncultured fungi with single-cell genomics

Area of Science:

• Mycology
• Genomics
• Bioinformatics

Background:

• Metagenomics provides community-level insights but often misses low-abundance fungi.
• Single-cell genomics (SCG) isolates individual cells or nuclei to generate single-amplified genomes (SAGs).
• SCG is crucial for accessing genomes from uncultured fungal lineages.

Purpose of the Study:

• To contrast metagenomics and SCG for fungal genome recovery.
• To categorize existing fungal SCG applications.
• To highlight SCG's value for strain resolution and genotypic context.

Main Methods:

• Categorization of SCG applications: spore-level sequencing, single-nucleus genomics, and single-spore sequencing.
• Analysis of pooling and co-assembly strategies for improved genome completeness.
• Review of practical advances in SCG, including QC triage and hybrid assembly.

Main Results:

• SCG excels at recovering rare or microdiverse fungal taxa.
• Pooling and co-assembly of cells enhance genome completeness.
• Key challenges include cell lysis, amplification bias, and contamination control.

Conclusions:

• SCG provides unique value for strain resolution, gene cluster recovery, and karyotype validation.
• Combined with metagenomics, SCG offers a strain-resolved view of fungal biodiversity.
• Ongoing SCG pipeline improvements promise routine access to genomes from diverse fungi.