CPL - Chalmers Publication Library
| Utbildning | Forskning | Styrkeområden | Om Chalmers | In English In English Ej inloggad.

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

M. R. Andersen ; M. P. Salazar ; P. J. Schaap ; P. J. I. Van De Vondervoort ; D. Culley ; J. Thykaer ; J. C. Frisvad ; K. F. Nielsen ; R. Albang ; K. Albermann ; R. M. Berka ; G. H. Braus ; S. A. Braus-Stromeyer ; L. M. Corrochano ; Z. Dai ; P. W. M. Van Dijck ; G. Hofmann ; L. L. Lasure ; J. K. Magnuson ; H. Menke ; M. Meijer ; S. L. Meijer ; J. B. Nielsen ; M. L. Nielsen ; A. J. J. Van Ooyen ; H. J. Pel ; L. Poulsen ; R. A. Samson ; H. Stam ; A. Tsang ; J. M. Van Den Brink ; A. Atkins ; A. Aerts ; H. Shapiro ; J. Pangilinan ; A. Salamov ; Y. Lou ; E. Lindquist ; S. Lucas ; J. Grimwood ; I. V. Grigoriev ; C. P. Kubicek ; D. Martinez ; N. N. M. E. Van Peij ; J. A. Roubos ; Jens B. Nielsen (Institutionen för kemi- och bioteknik, Systembiologi) ; S. E. Baker
Genome Research (1088-9051). Vol. 21 (2011), 6, p. 885-897.
[Artikel, refereegranskad vetenskaplig]

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

Nyckelord: Base Sequence, Computational Biology, Evolution, Molecular, Gene Expression Profiling, Gene Rearrangement, Gene Transfer, Horizontal, Genetic Variation, Genome

Den här publikationen ingår i följande styrkeområden:

Läs mer om Chalmers styrkeområden  

Denna post skapades 2012-09-21. Senast ändrad 2014-10-27.
CPL Pubid: 163677


Läs direkt!

Lokal fulltext (fritt tillgänglig)

Länk till annan sajt (kan kräva inloggning)

Institutioner (Chalmers)

Institutionen för kemi- och bioteknik, Systembiologi (2008-2014)


Hållbar utveckling

Chalmers infrastruktur