1 Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
2 US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
3 Amyris, Inc., Emeryville, CA, USA.
4 US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.
5 Sandia National Laboratory, Livermore, CA, USA.
6 Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
7 Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
8 Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.
9 Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.
10 Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
11 Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
12 Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
13 Department of Microbiology, University of Helsinki, Helsinki, Finland.
14 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
15 US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA. scott.baker@pnnl.gov.
16 Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. scott.baker@pnnl.gov.
17 Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark. mr@bio.dtu.dk.

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

Nat Genet. 2018 12;50(12):1688-1695

Authors: Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR

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.

PMID: 30349117 [PubMed - indexed for MEDLINE]