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Title: Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species

Abstract

The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories over model organisms to human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus and A. steynii) has been whole genome PacBio sequenced to provide genetic references in three Aspergillus sections. Additionally, A. taichungensis and A. candidus were sequenced for SM elucidation. Thirteen Aspergillus genomes were analysed with comparative genomics to determine phylogeny and genetic diversity, showing that each new genome contains 15–27% genes not found in other sequenced Aspergilli. In particular, the new species A. novofumigatus was compared to the pathogenic species A. fumigatus. This suggests that A. novofumigatus can produce most of the same allergens, virulence and pathogenicity factors as A. fumigatus suggesting that A. novofumigatus could be as pathogenic as A. fumigatus. Furthermore, SMs were linked to gene clusters based on biological and chemical knowledge and analysis, genome sequences and predictive algorithms.

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [3];  [1];  [2];  [1];  [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2] more »; ORCiD logo [4];  [5];  [1];  [1];  [6];  [7]; ORCiD logo [1] « less
  1. Technical Univ. of Denmark, Lyngby (Denmark)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Univ. of Manchester (United Kingdom)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  5. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1416221
Alternate Identifier(s):
OSTI ID: 1439668; OSTI ID: 1465428
Report Number(s):
PNNL-SA-131168
Journal ID: ISSN 0027-8424; 830403000
Grant/Contract Number:  
AC05-76RL01830; AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 4; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Aspergillus; fumigatus; comparative genomics; secondary metabolism

Citation Formats

Kjerbolling, Inge, Vesth, Tammi C., Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kuo, Alan, Bowyer, Paul, Matsuda, Yudai, Mondo, Stephen, Lyhne, Ellen K., Kogle, Martin E., Clum, Alicia, Lipzen, Anna, Salamov, Asaf, Ngan, Chew Yee, Daum, Chris, Chiniquy, Jennifer, Barry, Kerrie, LaButti, Kurt, Haridas, Sajeet, Simmons, Blake A., Magnuson, Jon K., Mortensen, Uffe H., Larsen, Thomas O., Grigoriev, Igor V., Baker, Scott E., and Andersen, Mikael R. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. United States: N. p., 2018. Web. doi:10.1073/pnas.1715954115.
Kjerbolling, Inge, Vesth, Tammi C., Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kuo, Alan, Bowyer, Paul, Matsuda, Yudai, Mondo, Stephen, Lyhne, Ellen K., Kogle, Martin E., Clum, Alicia, Lipzen, Anna, Salamov, Asaf, Ngan, Chew Yee, Daum, Chris, Chiniquy, Jennifer, Barry, Kerrie, LaButti, Kurt, Haridas, Sajeet, Simmons, Blake A., Magnuson, Jon K., Mortensen, Uffe H., Larsen, Thomas O., Grigoriev, Igor V., Baker, Scott E., & Andersen, Mikael R. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. United States. doi:10.1073/pnas.1715954115.
Kjerbolling, Inge, Vesth, Tammi C., Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kuo, Alan, Bowyer, Paul, Matsuda, Yudai, Mondo, Stephen, Lyhne, Ellen K., Kogle, Martin E., Clum, Alicia, Lipzen, Anna, Salamov, Asaf, Ngan, Chew Yee, Daum, Chris, Chiniquy, Jennifer, Barry, Kerrie, LaButti, Kurt, Haridas, Sajeet, Simmons, Blake A., Magnuson, Jon K., Mortensen, Uffe H., Larsen, Thomas O., Grigoriev, Igor V., Baker, Scott E., and Andersen, Mikael R. Tue . "Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species". United States. doi:10.1073/pnas.1715954115.
@article{osti_1416221,
title = {Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species},
author = {Kjerbolling, Inge and Vesth, Tammi C. and Frisvad, Jens C. and Nybo, Jane L. and Theobald, Sebastian and Kuo, Alan and Bowyer, Paul and Matsuda, Yudai and Mondo, Stephen and Lyhne, Ellen K. and Kogle, Martin E. and Clum, Alicia and Lipzen, Anna and Salamov, Asaf and Ngan, Chew Yee and Daum, Chris and Chiniquy, Jennifer and Barry, Kerrie and LaButti, Kurt and Haridas, Sajeet and Simmons, Blake A. and Magnuson, Jon K. and Mortensen, Uffe H. and Larsen, Thomas O. and Grigoriev, Igor V. and Baker, Scott E. and Andersen, Mikael R.},
abstractNote = {The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories over model organisms to human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus and A. steynii) has been whole genome PacBio sequenced to provide genetic references in three Aspergillus sections. Additionally, A. taichungensis and A. candidus were sequenced for SM elucidation. Thirteen Aspergillus genomes were analysed with comparative genomics to determine phylogeny and genetic diversity, showing that each new genome contains 15–27% genes not found in other sequenced Aspergilli. In particular, the new species A. novofumigatus was compared to the pathogenic species A. fumigatus. This suggests that A. novofumigatus can produce most of the same allergens, virulence and pathogenicity factors as A. fumigatus suggesting that A. novofumigatus could be as pathogenic as A. fumigatus. Furthermore, SMs were linked to gene clusters based on biological and chemical knowledge and analysis, genome sequences and predictive algorithms.},
doi = {10.1073/pnas.1715954115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 4,
volume = 115,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1073/pnas.1715954115

Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

Figures / Tables:

Table 1 Table 1: Overview of sequencing and annotation data for the four investigated PacBio-sequenced species, plus two additional Illumina-sequenced species

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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.