A comparative genomics study of 23 Aspergillus species from section Flavi
Abstract
Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.
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- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- Villium Foundation; Danish National Research Foundation; Villum Foundation; Jorck Foundation; USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1619580
- Alternate Identifier(s):
- OSTI ID: 1605144; OSTI ID: 1619163
- Report Number(s):
- PNNL-SA-146998
Journal ID: ISSN 2041-1723; 1106; PII: 14051
- Grant/Contract Number:
- AC02-05CH11231; VKR023437; DNRF137; AC05-76RL01830
- Resource Type:
- Published Article
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Name: Nature Communications Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Aspergillus; Section Flavi; Comparative Genomics; Secondary Metabolism aflatoxin; miyakamide; CAZyme; applied microbiology; fungal genomics; industrial microbiology; small molecules
Citation Formats
Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R. A comparative genomics study of 23 Aspergillus species from section Flavi. United Kingdom: N. p., 2020.
Web. doi:10.1038/s41467-019-14051-y.
Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., & Andersen, Mikael R. A comparative genomics study of 23 Aspergillus species from section Flavi. United Kingdom. https://doi.org/10.1038/s41467-019-14051-y
Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R. Thu .
"A comparative genomics study of 23 Aspergillus species from section Flavi". United Kingdom. https://doi.org/10.1038/s41467-019-14051-y.
@article{osti_1619580,
title = {A comparative genomics study of 23 Aspergillus species from section Flavi},
author = {Kjærbølling, Inge and Vesth, Tammi and Frisvad, Jens C. and Nybo, Jane L. and Theobald, Sebastian and Kildgaard, Sara and Petersen, Thomas Isbrandt and Kuo, Alan and Sato, Atsushi and Lyhne, Ellen K. and Kogle, Martin E. and Wiebenga, Ad and Kun, Roland S. and Lubbers, Ronnie J. M. and Mäkelä, Miia R. and Barry, Kerrie and Chovatia, Mansi and Clum, Alicia and Daum, Chris and Haridas, Sajeet and He, Guifen and LaButti, Kurt and Lipzen, Anna and Mondo, Stephen and Pangilinan, Jasmyn and Riley, Robert and Salamov, Asaf and Simmons, Blake A. and Magnuson, Jon K. and Henrissat, Bernard and Mortensen, Uffe H. and Larsen, Thomas O. and de Vries, Ronald P. and Grigoriev, Igor V. and Machida, Masayuki and Baker, Scott E. and Andersen, Mikael R.},
abstractNote = {Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.},
doi = {10.1038/s41467-019-14051-y},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United Kingdom},
year = {2020},
month = {2}
}
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Figures / Tables:
Fig. 1: Phylogeny and genome statistics of section Flavi plus eight other Aspergillus, Penicillium, and Neurospora species. a Phylogenetic tree constructed using RAxML, MUSCLE, and Gblocks based on 200 monocore genes (a single homolog in each of the species). The red star indicates an uncertain leaf most likely caused bymore »
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