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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. In order to learn more about fungal speciation, as well as potential for applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as six A. niger isolates. This allowed us to quantify both inter- and intra-species genomic variation. We further predicted 17,903 CAZymes 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 A. nidulans. Experimental and computational analyses all supported a role in speciation for secondary metabolism and regulators and allowed us to propose a three-step model for fungal speciation.

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1492689
Report Number(s):
PNNL-SA-133567
Journal ID: ISSN 1061-4036
DOE Contract Number:  
AC05-76RL01830
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:
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.
@article{osti_1492689,
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. In order to learn more about fungal speciation, as well as potential for applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as six A. niger isolates. This allowed us to quantify both inter- and intra-species genomic variation. We further predicted 17,903 CAZymes 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 A. nidulans. Experimental and computational analyses all supported a role in speciation for secondary metabolism and regulators and allowed us to propose a three-step model for fungal speciation.},
doi = {10.1038/s41588-018-0246-1},
journal = {Nature Genetics},
issn = {1061-4036},
number = 12,
volume = 50,
place = {United States},
year = {2018},
month = {10}
}