Complete genomes from single-cells of unculturable fungi

In recent years, environmental DNA (eDNA) has allowed us to identify large numbers of unculturable fungi and exime their diversity using “barcodes.” However, except for knowing that these species are present and generally how their ITS sequence relates to other fungi, we know very little about these cryptic organisms. Now researchers at the U.S. Department of Energy Joint Genome Institute have developed a pipeline that can generate genomes from single cells of uncultivated fungi.

This approach was applied to several early-diverging lineages including several mycoparasites. The single-cell approach yielded between 6 and 88% complete genomes for the eight species tested. However, combining single cells yielded co-assemblies that ranged for 73 to 99% complete.

This approach could help researchers study in more detail fungi that are known only from eDNA reads. With more complete genomes, we can learn much more about their metabolism and phylogenetic position than from possible ITS barcodes. The authors state that what they hope to see happen is that other researchers pick up this approach and tweak the pipeline to optimize it for different groups.


Story: DOE/Lawrence Berkeley National Laboratory. “Expanding fungal diversity, one cell at a time: Pilot study demonstrates single cell genomics approach for fungal genomic diversity.” ScienceDaily. ScienceDaily, 8 October 2018. <>.

Journal: Steven R. Ahrendt, C. Alisha Quandt, Doina Ciobanu, Alicia Clum, Asaf Salamov, Bill Andreopoulos, Jan-Fang Cheng, Tanja Woyke, Adrian Pelin, Bernard Henrissat, Nicole K. Reynolds, Gerald L. Benny, Matthew E. Smith, Timothy Y. James, Igor V. Grigoriev. Leveraging single-cell genomics to expand the fungal tree of life. Nature Microbiology, 2018; DOI: 10.1038/s41564-018-0261-0.



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