Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius
Abstract
In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involved in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis.
- Authors:
-
- Univ. Autònoma de Barcelona, Bellaterra, Catalonia (Spain)
- Sequentia Biotech SL, Barcelona, Catalonia (Spain)
- Publication Date:
- Research Org.:
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia (Spain)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Contributing Org.:
- Joint Genome Institute, Walnut Creek, CA (United States)
- OSTI Identifier:
- 1215424
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 5; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; fungal genomics; gene regulatory networks
Citation Formats
Cabañes, F. Javier, Sanseverino, Walter, Castellá, Gemma, Bragulat, M. Rosa, Cigliano, Riccardo Aiese, and Sánchez, Armand. Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius. United States: N. p., 2015.
Web. doi:10.1038/srep09086.
Cabañes, F. Javier, Sanseverino, Walter, Castellá, Gemma, Bragulat, M. Rosa, Cigliano, Riccardo Aiese, & Sánchez, Armand. Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius. United States. https://doi.org/10.1038/srep09086
Cabañes, F. Javier, Sanseverino, Walter, Castellá, Gemma, Bragulat, M. Rosa, Cigliano, Riccardo Aiese, and Sánchez, Armand. Fri .
"Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius". United States. https://doi.org/10.1038/srep09086. https://www.osti.gov/servlets/purl/1215424.
@article{osti_1215424,
title = {Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius},
author = {Cabañes, F. Javier and Sanseverino, Walter and Castellá, Gemma and Bragulat, M. Rosa and Cigliano, Riccardo Aiese and Sánchez, Armand},
abstractNote = {In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involved in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis.},
doi = {10.1038/srep09086},
journal = {Scientific Reports},
number = ,
volume = 5,
place = {United States},
year = {2015},
month = {3}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 13 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Non-aflatoxigenic Aspergillus flavus to prevent aflatoxin contamination in crops: advantages and limitations
journal, January 2014
- Ehrlich, Kenneth C.
- Frontiers in Microbiology, Vol. 5
A polyketide synthase gene required for ochratoxin A biosynthesis in Aspergillus ochraceus
journal, December 2003
- O'Callaghan, J.; Caddick, M. X.; Dobson, A. D. W.
- Microbiology, Vol. 149, Issue 12
Development of a Real Time PCR System for Detection of Penicillium nordicum and for Monitoring Ochratoxin A Production in Foods by Targeting the Ochratoxin Polyketide Synthase Gene
journal, January 2004
- Geisen, Rolf; Mayer, Zsuzsanna; Karolewiez, Anja
- Systematic and Applied Microbiology, Vol. 27, Issue 4
Comprehensive molecular system to study the presence, growth and ochratoxin A biosynthesis of Penicillium verrucosum in wheat
journal, August 2008
- Schmidt-Heydt, M.; Richter, W.; Michulec, M.
- Food Additives & Contaminants: Part A, Vol. 25, Issue 8
Aspergillus westerdijkiae polyketide synthase gene “aoks1” is involved in the biosynthesis of ochratoxin A
journal, January 2009
- Bacha, N.; Atoui, A.; Mathieu, F.
- Fungal Genetics and Biology, Vol. 46, Issue 1
Functional characterization of the polyketide synthase gene required for ochratoxin A biosynthesis in Penicillium verrucosum
journal, February 2013
- O'Callaghan, John; Coghlan, Avril; Abbas, Abdelhamid
- International Journal of Food Microbiology, Vol. 161, Issue 3
New Insight into the Ochratoxin A Biosynthetic Pathway through Deletion of a Nonribosomal Peptide Synthetase Gene in Aspergillus carbonarius
journal, September 2012
- Gallo, Antonia; Bruno, Kenneth S.; Solfrizzo, Michele
- Applied and Environmental Microbiology, Vol. 78, Issue 23
Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius
journal, June 2014
- Gallo, Antonia; Knox, Benjamin P.; Bruno, Kenneth S.
- International Journal of Food Microbiology, Vol. 179
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
journal, November 2013
- Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge
- Nucleic Acids Research, Vol. 42, Issue D1
An integrated semiconductor device enabling non-optical genome sequencing
journal, July 2011
- Rothberg, Jonathan M.; Hinz, Wolfgang; Rearick, Todd M.
- Nature, Vol. 475, Issue 7356
Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology
journal, July 2011
- Mellmann, Alexander; Harmsen, Dag; Cummings, Craig A.
- PLoS ONE, Vol. 6, Issue 7
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
journal, January 2007
- Pel, Herman J.; de Winde, Johannes H.; Archer, David B.
- Nature Biotechnology, Vol. 25, Issue 2, p. 221-231
Characterization of nonochratoxigenic strains of Aspergillus carbonarius from grapes
journal, December 2013
- Cabañes, F. J.; Bragulat, M. R.; Castellá, G.
- Food Microbiology, Vol. 36, Issue 2
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
journal, January 2012
- Quail, Michael; Smith, Miriam E.; Coupland, Paul
- BMC Genomics, Vol. 13, Article No. 341
Performance comparison of benchtop high-throughput sequencing platforms
journal, April 2012
- Loman, Nicholas J.; Misra, Raju V.; Dallman, Timothy J.
- Nature Biotechnology, Vol. 30, Issue 5
An easy screening method for fungi producing ochratoxin A in pure culture
journal, December 2001
- Bragulat, M. R.; Abarca, M. L.; Cabañes, F. J.
- International Journal of Food Microbiology, Vol. 71, Issue 2-3
Ochratoxin A and citrinin producing species of the genus Penicillium from feedstuffs
journal, August 2008
- Bragulat, M.; Martinez, E.; Castella, G.
- International Journal of Food Microbiology, Vol. 126, Issue 1-2
Primer3—new capabilities and interfaces
journal, June 2012
- Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu
- Nucleic Acids Research, Vol. 40, Issue 15
Clustal W and Clustal X version 2.0
journal, September 2007
- Larkin, M. A.; Blackshields, G.; Brown, N. P.
- Bioinformatics, Vol. 23, Issue 21, p. 2947-2948
A survey of tools for variant analysis of next-generation genome sequencing data
journal, January 2013
- Pabinger, S.; Dander, A.; Fischer, M.
- Briefings in Bioinformatics, Vol. 15, Issue 2
Genome structural variation discovery and genotyping
journal, March 2011
- Alkan, Can; Coe, Bradley P.; Eichler, Evan E.
- Nature Reviews Genetics, Vol. 12, Issue 5
Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011
- Martin, Marcel
- EMBnet.journal, Vol. 17, Issue 1
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift
journal, January 2012
- Cingolani, Pablo; Patel, Viral M.; Coon, Melissa
- Frontiers in Genetics, Vol. 3
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w
journal, April 2012
- Cingolani, Pablo; Platts, Adrian; Wang, Le Lily
- Fly, Vol. 6, Issue 2
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
journal, February 2011
- Abyzov, A.; Urban, A. E.; Snyder, M.
- Genome Research, Vol. 21, Issue 6
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
journal, August 2005
- Conesa, A.; Gotz, S.; Garcia-Gomez, J. M.
- Bioinformatics, Vol. 21, Issue 18
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
journal, July 2011
- Supek, Fran; Bošnjak, Matko; Škunca, Nives
- PLoS ONE, Vol. 6, Issue 7
Works referencing / citing this record:
Specific antigen‐based and emerging detection technologies of mycotoxins
journal, April 2019
- Rahman, Hamid Ur; Yue, Xiaofeng; Yu, Qiuyu
- Journal of the Science of Food and Agriculture, Vol. 99, Issue 11
Genomic diversity in ochratoxigenic and non ochratoxigenic strains of Aspergillus carbonarius
journal, April 2018
- Castellá, Gemma; Bragulat, M. Rosa; Puig, Laura
- Scientific Reports, Vol. 8, Issue 1
Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential
journal, March 2018
- Choque, Elodie; Klopp, Christophe; Valiere, Sophie
- BMC Genomics, Vol. 19, Issue 1
Study on the presence of ochratoxin α in cultures of ochratoxigenic and non- ochratoxigenic strains of Aspergillus carbonarius
journal, October 2017
- Bragulat, M. Rosa; Eustaquio, Alba; Cabañes, F. Javier
- PLOS ONE, Vol. 12, Issue 10
Current Status and Future Opportunities of Omics Tools in Mycotoxin Research
journal, October 2018
- Eshelli, Manal; Qader, M.; Jambi, Ebtihaj
- Toxins, Vol. 10, Issue 11