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

Autor: M. Meijer, Herman Jan Pel, Jasmyn Pangilinan, Jette Thykaer, Gerhard H. Braus, Scott E. Baker, Rob Samson, Jens Christian Frisvad, Kristian Fog Nielsen, Erika Lindquist, Susanna A. Braus-Stromeyer, Margarita Salazar, Peter J. I. van de Vondervoort, Peter J. Schaap, Michael Lynge Nielsen, Diego Martinez, Susan Lisette Meijer, Johannes Maarten Van Den Brink, Jakob Blæsbjerg Nielsen, Johannes Andries Roubos, Hein Stam, Jon K. Magnuson, Noël Nicolaas Maria Elisabeth Van Peij, Lars Kongsbak Poulsen, Adrian Tsang, Alex Atkins, Asaf Salamov, Ziyu Dai, Jane Grimwood, Harris Shapiro, Igor V. Grigoriev, Piet W.M. van Dijck, Susan Lucas, Andrea Aerts, Luis M. Corrochano, Hildegard Henna Menke, Albert J. J. van Ooyen, David E. Culley, Gerald Hofmann, Mikael Rørdam Andersen, Randy M. Berka, Jens Nielsen, Linda L. Lasure, Yigong Lou, Kaj Albermann, Christian P. Kubicek, Richard Albang
Přispěvatelé: Universidad de Sevilla. Departamento de Genética
Jazyk: angličtina
Rok vydání: 2011
Předmět:
Genome
Citric acid
Glucan 1
liquid-chromatography
Systems and Synthetic Biology
Phylogeny
Genetics (clinical)
Gene Rearrangement
2. Zero hunger
Genetics
Systeem en Synthetische Biologie
0303 health sciences
biology
Fungal genetics
Genomics
saccharomyces-cerevisiae
Aspergillus niger
Genome
Fungal
Transfer RNA
recognition
Gene Transfer
Horizontal
Sequence analysis
Molecular Sequence Data
linkage group
Polymorphism
Single Nucleotide
Synteny
Evolution
Molecular
03 medical and health sciences
Species Specificity
mycotoxins
expression
4 alpha glucosidase
Gene
VLAG
030304 developmental biology
Whole genome sequencing
Comparative genomics
Base Sequence
030306 microbiology
Research
Gene Expression Profiling
Computational Biology
Genetic Variation
fungal metabolite
Sequence Analysis
DNA
biology.organism_classification
karyotype
gene ontology
identification
Zdroj: Genome Research 21 (2011) 6
idUS. Depósito de Investigación de la Universidad de Sevilla
instname
Genome Research, 21(6), 885-897. Cold Spring Harbor Laboratory Press
Genome Research, 21(6), 885-897
ISSN: 1088-9051
Popis: 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 whole-genome 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.
Databáze: OpenAIRE
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