ArticleGenome research2011
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 papers, 1 of them a synthesis that pooled it.
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Who cites it
187 citing papers in PubMed, 1 synthesis or guideline pooled it, 363 citations in OpenAlex.
- Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.Nucleic acids research · 2019Pooled it
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- Research Advances on the Functions of Transcriptional Regulators in Filamentous Fungi.Microorganisms · 2026Review
- Draft genome assembly of hyper citric acid-producing Aspergillus niger mutant strain developed through gamma radiation bombardment.BMC genomic data · 2026Article
- Improved genome assembly ofMicrobiology resource announcements · 2026Article
- Expanding the genetic toolkit: adenine and cytosine base editors for gene disruption in Aspergillus niger.Microbial cell factories · 2026Article
- Identification and characterization of a novel transcriptional factor Spt7 involved in conidia formation and mycelium development in Aspergillus niger.BMC microbiology · 2026Article
- An examination of the quinic acid utilization genes in Aspergillus niger reveals the involvement of 2 pH-dependent permeases.G3 (Bethesda, Md.) · 2025Article
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- Metarhizium spp. encode an ochratoxin cluster and a high efficiency ochratoxin-degrading amidohydrolase revealed by genomic analysis.Journal of advanced research · 2025Article
- Section-level genome sequencing and comparative genomics ofStudies in mycology · 2025Article
- FunFEA: an R package for fungal functional enrichment analysis.BMC bioinformatics · 2025Article
- Adaptability assessment of Aspergillus niger and Aspergillus terreus isolated from long-term municipal/industrial effluent-irrigated soils to cadmium stress.BMC microbiology · 2025Article
- Whole genome sequence, CAZyme repertoire and sugar metabolic model of the phytopathogenic fungus Kretzschmaria zonata GFP 132.Molecular genetics and genomics : MGG · 2025Article
- Multiomic Analysis Provided Insights into the Responses of Carbon Sources by Wood-Rotting FungiJournal of fungi (Basel, Switzerland) · 2025Article
- Article
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- Safety evaluation of the food enzyme carboxypeptidase C from the genetically modifiedEFSA journal. European Food Safety Authority · 2024Article
- NHEJ and HDR can occur simultaneously during gene integration into the genome of Aspergillus niger.Fungal biology and biotechnology · 2024Article
127 more citing papers are in PubMed but not listed here.
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Authors and funding
47 authors at 16 institutions in 7 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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