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

Tammi C. Vesth 1 Jane Nybo 1 Sebastian Theobald 1 Jens Frisvad 1 Thomas Larsen 1 Kristian Nielsen 1 Jakob Hoof 1 Julian Brandl 1 Asaf Salamov 2 Robert Riley 2 John Gladden 3 Pallavi Phatale 3 Morten Nielsen 1 Ellen Lyhne 1 Martin Kogle 1 Kimchi Strasser 4 Erin Mcdonnell 4 Kerrie Barry 2 Alicia Clum 2 Cindy Chen 2 Kurt Labutti 5 Sajeet Haridas 2 Matt Nolan 2 Laura Sandor 2 Alan Kuo 5 Anna Lipzen 5 Matthieu Hainaut 6 Elodie Drula 7 Adrian Tsang 4 Jon Magnuson 8 Bernard Henrissat 6 Ad Wiebenga 9 Blake Simmons 8 Miia Mäkelä 9 Ronald de Vries 9 Igor Grigoriev 10 Uffe Mortensen 1 Scott Baker 8 Mikael Handersen 1
1 DTU - Technical University of Denmark [Lyngby]
2 United States Department of Energy Joint Genome Institute
3 United States Department of Energy Joint BioEnergy Institute
4 Concordia University [Montreal]
5 US Department of Energy Joint Genome Institute
6 AFMB - Architecture et fonction des macromolécules biologiques
7 BBF - Biodiversité et Biotechnologie Fongiques
8 US Department of Energy Joint BioEnergy Institute
9 Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal
10 US Department of Energy Joint Genome Institute, Walnut Creek CA, USA
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.
Keywords : fungi pathway aligment prediction dereplication ochratoxin-a
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Tammi C. Vesth, Jane Nybo, Sebastian Theobald, Jens Frisvad, Thomas Larsen, et al.. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics, Nature Publishing Group, 2018, 50 (12), pp.1688-1695. ⟨10.1038/s41588-018-0246-1⟩. ⟨hal-02094492⟩

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