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

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.

Authors:
 [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [1];  [1];  [2];  [3]; ORCiD logo [4];  [5];  [1];  [1];  [1];  [6];  [6];  [2];  [2];  [2] more »;  [2];  [2];  [2];  [2];  [2];  [2];  [7];  [7];  [6];  [5];  [8];  [9]; ORCiD logo [10]; ORCiD logo [11];  [9]; ORCiD logo [12]; ORCiD logo [1];  [5]; ORCiD logo [1] « less
  1. Technical Univ. of Denmark, Kongens Lyngby (Denmark)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Amyris, Inc., Emeryville, CA (United States)
  4. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  5. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  6. Concordia Univ., Montreal, QC (Canada)
  7. Aix-Marseille Univ., Marseille (France); Inst. National de la Recherche Agronomique, Marseille (France)
  8. Aix-Marseille Univ., Marseille (France); Inst. National de la Recherche Agronomique, Marseille (France); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  9. Utrecht Univ., Utrecht (The Netherlands)
  10. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  11. Utrecht Univ., Utrecht (The Netherlands); Univ. of Helsinki (Finland)
  12. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Danish National Research Foundation (DNRF); Novo Nordisk Foundation
OSTI Identifier:
1532285
DOE Contract Number:  
AC02-05CH11231; AC05-76RL01830; NNF13OC0005201; NNF13OC0004831
Resource Type:
Journal Article
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 50; Journal Issue: 12; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genomics; fungi; Aspergillus; Nigri; Primary Metabolism; Secondary Metabolism; CAZyme

Citation Formats

Vesth, Tammi C., Nybo, Jane L., Theobald, Sebastian, Frisvad, Jens C., Larsen, Thomas O., Nielsen, Kristian F., Hoof, Jakob B., Brandl, Julian, Salamov, Asaf, Riley, Robert, Gladden, John M., Phatale, Pallavi, Nielsen, Morten T., Lyhne, Ellen K., Kogle, Martin E., Strasser, Kimchi, McDonnell, Erin, Barry, Kerrie, Clum, Alicia, Chen, Cindy, LaButti, Kurt, Haridas, Sajeet, Nolan, Matt, Sandor, Laura, Kuo, Alan, Lipzen, Anna, Hainaut, Matthieu, Drula, Elodie, Tsang, Adrian, Magnuson, Jon K., Henrissat, Bernard, Wiebenga, Ad, Simmons, Blake A., Mäkelä, Miia R., de Vries, Ronald P., Grigoriev, Igor V., Mortensen, Uffe H., Baker, Scott E., and Andersen, Mikael R. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. United States: N. p., 2018. Web. doi:10.1038/s41588-018-0246-1.
Vesth, Tammi C., Nybo, Jane L., Theobald, Sebastian, Frisvad, Jens C., Larsen, Thomas O., Nielsen, Kristian F., Hoof, Jakob B., Brandl, Julian, Salamov, Asaf, Riley, Robert, Gladden, John M., Phatale, Pallavi, Nielsen, Morten T., Lyhne, Ellen K., Kogle, Martin E., Strasser, Kimchi, McDonnell, Erin, Barry, Kerrie, Clum, Alicia, Chen, Cindy, LaButti, Kurt, Haridas, Sajeet, Nolan, Matt, Sandor, Laura, Kuo, Alan, Lipzen, Anna, Hainaut, Matthieu, Drula, Elodie, Tsang, Adrian, Magnuson, Jon K., Henrissat, Bernard, Wiebenga, Ad, Simmons, Blake A., Mäkelä, Miia R., de Vries, Ronald P., Grigoriev, Igor V., Mortensen, Uffe H., Baker, Scott E., & Andersen, Mikael R. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. United States. doi:10.1038/s41588-018-0246-1.
Vesth, Tammi C., Nybo, Jane L., Theobald, Sebastian, Frisvad, Jens C., Larsen, Thomas O., Nielsen, Kristian F., Hoof, Jakob B., Brandl, Julian, Salamov, Asaf, Riley, Robert, Gladden, John M., Phatale, Pallavi, Nielsen, Morten T., Lyhne, Ellen K., Kogle, Martin E., Strasser, Kimchi, McDonnell, Erin, Barry, Kerrie, Clum, Alicia, Chen, Cindy, LaButti, Kurt, Haridas, Sajeet, Nolan, Matt, Sandor, Laura, Kuo, Alan, Lipzen, Anna, Hainaut, Matthieu, Drula, Elodie, Tsang, Adrian, Magnuson, Jon K., Henrissat, Bernard, Wiebenga, Ad, Simmons, Blake A., Mäkelä, Miia R., de Vries, Ronald P., Grigoriev, Igor V., Mortensen, Uffe H., Baker, Scott E., and Andersen, Mikael R. Mon . "Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri". United States. doi:10.1038/s41588-018-0246-1. https://www.osti.gov/servlets/purl/1532285.
@article{osti_1532285,
title = {Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri},
author = {Vesth, Tammi C. and Nybo, Jane L. and Theobald, Sebastian and Frisvad, Jens C. and Larsen, Thomas O. and Nielsen, Kristian F. and Hoof, Jakob B. and Brandl, Julian and Salamov, Asaf and Riley, Robert and Gladden, John M. and Phatale, Pallavi and Nielsen, Morten T. and Lyhne, Ellen K. and Kogle, Martin E. and Strasser, Kimchi and McDonnell, Erin and Barry, Kerrie and Clum, Alicia and Chen, Cindy and LaButti, Kurt and Haridas, Sajeet and Nolan, Matt and Sandor, Laura and Kuo, Alan and Lipzen, Anna and Hainaut, Matthieu and Drula, Elodie and Tsang, Adrian and Magnuson, Jon K. and Henrissat, Bernard and Wiebenga, Ad and Simmons, Blake A. and Mäkelä, Miia R. and de Vries, Ronald P. and Grigoriev, Igor V. and Mortensen, Uffe H. and Baker, Scott E. and Andersen, Mikael R.},
abstractNote = {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.},
doi = {10.1038/s41588-018-0246-1},
journal = {Nature Genetics},
issn = {1061-4036},
number = 12,
volume = 50,
place = {United States},
year = {2018},
month = {10}
}

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