More than a million species of fungi are estimated to live on this planet, but most of that diversity remains unknown because the fungi have avoided detection and have not been cultured for study in laboratories. Through projects such as JGI’s 1000 Fungal Genomes, researchers aim to expand the known fraction of fungal diversity with representative genome sequences for various lineages. Even with such efforts though, the majority of available genomes belong to just two major lineages, Ascomycota and Basidiomycota. The early-diverging lineages that are closer to the base of the Fungal Tree of Life have few representative genomes.

Now, a team led by researchers at the Joint Genome Institute has developed a pipeline to generate genomes from single cells of uncultivated fungi. The single-cell genomics approach was applied to eight fungi, seven of which belong to the early diverging lineages Cryptomycota, Chytridiomycota, and Zoopagomycota. In addition, six of the seven fungi are mycoparasites, or fungi that attack other fungi, which JGI data scientist and first author Steven Ahrendt noted might be a factor in why these species are unculturable.

The fungal single cells yielded anywhere from 6 percent of the genome to 88 percent, but combining the single cells yielded genome co-assemblies ranging from 73 percent complete up to 99 percent complete. “This work was a proof-of-principle that the single-cell genomics approach can reconstruct near-complete fungal genomes and provide insights into phylogenetic position and metabolic capacities of diverse unculturable species from environmental samples,” said JGI Fungal Program head and co-senior author Igor Grigoriev.

Read more in the JGI News Release.