Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Tammi Camilla Vesth, Jane L Nybo, Sebastian Theobald, Jens Christian Frisvad, Thomas Ostenfeld Larsen, Kristian Fog Nielsen, Jakob Blæsbjerg Hoof, Julian Brandl, Asaf Salamov, Robert Riley, John M Gladden, Pallavi Phatale, Morten T. Nielsen, Ellen K. Lyhne, Martin Engelhard Kogle, Kimchi Strasser, Erin McDonnell, Kerrie Barry, Alicia Clum, Cindy ChenKurt LaButti, Sajeet Haridas, Matt Nolan, Laura Sandor, Alan Kuo, Anna Lipzen, Matthieu Hainaut, Elodie Drula, Adrian Tsang, Jon K Magnuson, Bernard Henrissat, Ad Wiebenga, Blake A Simmons, Miia R Mäkelä, Ronald P de Vries, Igor V Grigoriev, Uffe Hasbro Mortensen, Scott E Baker, Mikael Rørdam Andersen*

*Corresponding author for this work

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Abstract

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.
Original languageEnglish
JournalNature Genetics
Volume50
Pages (from-to)1688–1695
ISSN1061-4036
DOIs
Publication statusPublished - 2018

Cite this

Vesth, T. C., Nybo, J. L., Theobald, S., Frisvad, J. C., Larsen, T. O., Nielsen, K. F., Hoof, J. B., Brandl, J., Salamov, A., Riley, R., Gladden, J. M., Phatale, P., Nielsen, M. T., Lyhne, E. K., Kogle, M. E., Strasser, K., McDonnell, E., Barry, K., Clum, A., ... Andersen, M. R. (2018). Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics, 50, 1688–1695. https://doi.org/10.1038/s41588-018-0246-1