Search: onr:"swepub:oai:research.chalmers.se:538bef5a-e425-4ed1-ab8a-24dc2d322a33" >
Comparative genomic...
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
-
- Andersen, M. R. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Salazar Pena, Margarita, 1979 (author)
- Danmarks Tekniske Universitet,Technical University of Denmark,Chalmers tekniska högskola,Chalmers University of Technology
-
- Schaap, P. J. (author)
- Wageningen University and Research
-
show more...
-
- Van De Vondervoort, P. J. I. (author)
- DSM Biotechnology Centre
-
- Culley, D. (author)
- Pacific Northwest National Laboratory
-
- Thykaer, J. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Frisvad, J. C. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Nielsen, K. F. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Albang, R. (author)
- Biomax Informatics AG
-
- Albermann, K. (author)
- Biomax Informatics AG
-
- Berka, R. M. (author)
- Novozymes, Inc.
-
- Braus, G. H. (author)
- Georg-August-Universität Göttingen,University of Göttingen
-
- Braus-Stromeyer, S. A. (author)
- Georg-August-Universität Göttingen,University of Göttingen
-
- Corrochano, L. M. (author)
- Universidad de Sevilla,University of Seville
-
- Dai, Z. (author)
- Pacific Northwest National Laboratory
-
- Van Dijck, P. W. M. (author)
- DSM Nutritional Products Ltd
-
- Hofmann, G. (author)
- Novozymes A/S
-
- Lasure, L. L. (author)
- Pacific Northwest National Laboratory
-
- Magnuson, J. K. (author)
- Pacific Northwest National Laboratory
-
- Menke, H. (author)
- DSM Biotechnology Centre
-
Meijer, M. (author)
-
- Meijer, S. L. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Nielsen, J. B. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Nielsen, M. L. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
- Van Ooyen, A. J. J. (author)
- DSM Biotechnology Centre
-
- Pel, H. J. (author)
- DSM Biotechnology Centre
-
- Poulsen, L. (author)
- Danmarks Tekniske Universitet,Technical University of Denmark
-
Samson, R. A. (author)
-
- Stam, H. (author)
- DSM Biotechnology Centre
-
- Tsang, A. (author)
- Université Concordia,Concordia University
-
- Van Den Brink, J. M. (author)
- Chr. Hansen Holding A/S
-
- Atkins, A. (author)
- DOE Joint Genome Institute
-
- Aerts, A. (author)
- DOE Joint Genome Institute
-
- Shapiro, H. (author)
- DOE Joint Genome Institute
-
- Pangilinan, J. (author)
- DOE Joint Genome Institute
-
- Salamov, A. (author)
- DOE Joint Genome Institute
-
- Lou, Y. (author)
- DOE Joint Genome Institute
-
- Lindquist, E. (author)
- DOE Joint Genome Institute
-
- Lucas, S. (author)
- DOE Joint Genome Institute
-
- Grimwood, J. (author)
- Stanford University
-
- Grigoriev, I. V. (author)
- DOE Joint Genome Institute
-
- Kubicek, C. P. (author)
- Technische Universität Wien,Vienna University of Technology
-
- Martinez, D. (author)
- Los Alamos National Laboratory,University of New Mexico
-
- Van Peij, N. N. M. E. (author)
- DSM Biotechnology Centre
-
- Roubos, J. A. (author)
- DSM Biotechnology Centre
-
- Nielsen, Jens B, 1962 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
-
- Baker, S. E. (author)
- Pacific Northwest National Laboratory
-
show less...
-
(creator_code:org_t)
- 2011-05-04
- 2011
- English.
-
In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 21:6, s. 885-897
- Related links:
-
http://publications.... (primary) (free)
-
show more...
-
http://genome.cshlp....
-
https://research.cha...
-
https://doi.org/10.1...
-
show less...
Abstract
Subject headings
Close
- The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook wholegenome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Gene Rearrangement
- Gene Transfer
- Gene Expression Profiling
- Base Sequence
- Evolution
- Molecular
- Genome
- Horizontal
- Computational Biology
- Genetic Variation
Publication and Content Type
- art (subject category)
- ref (subject category)
Find in a library
To the university's database
- By the author/editor
-
Andersen, M. R.
-
Salazar Pena, Ma ...
-
Schaap, P. J.
-
Van De Vondervoo ...
-
Culley, D.
-
Thykaer, J.
-
show more...
-
Frisvad, J. C.
-
Nielsen, K. F.
-
Albang, R.
-
Albermann, K.
-
Berka, R. M.
-
Braus, G. H.
-
Braus-Stromeyer, ...
-
Corrochano, L. M ...
-
Dai, Z.
-
Van Dijck, P. W. ...
-
Hofmann, G.
-
Lasure, L. L.
-
Magnuson, J. K.
-
Menke, H.
-
Meijer, M.
-
Meijer, S. L.
-
Nielsen, J. B.
-
Nielsen, M. L.
-
Van Ooyen, A. J. ...
-
Pel, H. J.
-
Poulsen, L.
-
Samson, R. A.
-
Stam, H.
-
Tsang, A.
-
Van Den Brink, J ...
-
Atkins, A.
-
Aerts, A.
-
Shapiro, H.
-
Pangilinan, J.
-
Salamov, A.
-
Lou, Y.
-
Lindquist, E.
-
Lucas, S.
-
Grimwood, J.
-
Grigoriev, I. V.
-
Kubicek, C. P.
-
Martinez, D.
-
Van Peij, N. N. ...
-
Roubos, J. A.
-
Nielsen, Jens B, ...
-
Baker, S. E.
-
show less...
- About the subject
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Genetics
- Articles in the publication
-
Genome Research
- By the university
-
Chalmers University of Technology