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Isolation of Culturable Yeasts and Molds from Soils to Investigate Fungal Population Structure
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A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species.

Mikael R Andersen1, Wanwipa Vongsangnak, Gianni Panagiotou

  • 1Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.

Proceedings of the National Academy of Sciences of the United States of America
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Researchers developed a new microarray for studying Aspergillus fungi transcriptomes. This tool identified conserved genes responding to xylose, revealing insights into complex carbohydrate metabolism across species.

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Area of Science:

  • Mycology
  • Genomics
  • Systems Biology

Background:

  • Full-genome sequencing of Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae enables systemic cellular physiology studies.
  • Transcriptome analysis is crucial for understanding fungal gene expression and cellular responses.

Purpose of the Study:

  • To introduce a validated Affymetrix GeneChip for transcriptome analysis of three Aspergillus species.
  • To explore conserved gene responses and regulatory mechanisms across these species using comparative transcriptomics.

Main Methods:

  • Development and validation of a custom Affymetrix GeneChip for Aspergillus transcriptome analysis.
  • Transcriptome profiling of Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae on glucose and xylose media.
  • Comparative gene expression analysis and promoter analysis across species.

Main Results:

  • The microarray effectively analyzed transcriptomes of the three Aspergillus species.
  • Twenty-three conserved genes, including the xylose transcriptional activator XlnR, were identified in response to xylose.
  • A conserved XlnR-binding site (5'-GGNTAAA-3') was identified in the promoters of up-regulated genes.

Conclusions:

  • The developed GeneChip is a validated tool for Aspergillus transcriptome studies.
  • Xylose triggers a conserved gene set, suggesting its role in indicating complex carbohydrate presence and inducing degrading enzymes.
  • Comparative transcriptomics provides a methodology for cross-species evolutionary studies within the Aspergillus genus.