ArticleProceedings of the National Academy of Sciences of the United States of America2008
A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it, 122 citations in OpenAlex.
- Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.Nucleic acids research · 2019Pooled it
- Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression during Tannin Biodegredation byInternational journal of molecular sciences · 2024Article
- Mutations in the Second Alternative Oxidase Gene: A New Approach to GroupJournal of fungi (Basel, Switzerland) · 2023Article
- Improving citric acid production of an industrial Aspergillus niger CGMCC 10142: identification and overexpression of a high-affinity glucose transporter with different promoters.Microbial cell factories · 2021Article
- Alternative transcription start sites of the enolase-encoding gene enoA are stringently used in glycolytic/gluconeogenic conditions in Aspergillus oryzae.Current genetics · 2020Article
- Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes inFrontiers in bioengineering and biotechnology · 2020Article
- Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era.Microbial cell factories · 2019Review
- Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule.Microbial cell factories · 2019Article
- Regulation of the Gα-cAMP/PKA signaling pathway in cellulose utilization of Chaetomium globosum.Microbial cell factories · 2018Article
- Comparative transcriptomics reveals specific responding genes associated with atherosclerosis in rabbit and mouse models.PloS one · 2018Article
- Analysis of the Transcriptome inFrontiers in bioengineering and biotechnology · 2018Article
- A community-driven reconstruction of theFungal biology and biotechnology · 2018Article
- Article
- A Highly Efficient Xylan-Utilization System inFrontiers in microbiology · 2018Article
- Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei.BMC genomics · 2017Article
- Regulators of plant biomass degradation in ascomycetous fungi.Biotechnology for biofuels · 2017Review
- Development and validation of a custom microarray for global transcriptome profiling of the fungus Aspergillus nidulans.Current genetics · 2016Article
- FunGeneClusterS: Predicting fungal gene clusters from genome and transcriptome data.Synthetic and systems biotechnology · 2016Article
- Lytic polysaccharide monooxygenases and other oxidative enzymes are abundantly secreted by Aspergillus nidulans grown on different starches.Biotechnology for biofuels · 2016Article
- Transcriptome Profile Analysis from Different Sex Types of Ginkgo biloba L.Frontiers in plant science · 2016Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance of the microarray. Gene comparisons of all three species and cross-analysis with the expression data identified 23 genes to be a conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. A promoter analysis of the up-regulated genes in all three species indicates the conserved XlnR-binding site to be 5'-GGNTAAA-3'. The composition of the conserved gene-set suggests that xylose acts as a molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross-species evolutionary studies within a genus using comparative transcriptomics.
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