Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes

Andrew H. Sims, Manda E. Gent, Geoffrey D. Robson, Nigel S. Dunn-Coleman, Stephen G. Oliver

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Whole genome sequencing of several filamentous ascomycetes is complete or in progress; these species, such as Aspergillus nidulans, are relatives of Saccharomyces cerevisiae. However, their genomes are much larger and their gene structure more complex, with genes often containing multiple introns. Automated annotation programs can quickly identify open reading frames for hypothetical genes, many of which will be conserved across large evolutionary distances, but further information is required to confirm functional assignments. We describe a comparative and functional genomics approach using sequence alignments and gene expression data to predict the function of Aspergillus nidulans genes. By highlighting examples of discrepancies between the automated genome annotation and cDNA or EST sequencing, we demonstrate that the greater complexity of gene structure in filamentous fungi demands independent data on gene expression and the gene sequence be used to make confident functional assignments.
    Original languageEnglish
    Pages (from-to)853-857
    Number of pages4
    JournalMycological Research
    Volume108
    Issue number8
    DOIs
    Publication statusPublished - Aug 2004

    Keywords

    • enzymology: Aspergillus nidulans
    • genetics: DNA, Complementary
    • genetics: DNA, Fungal
    • Exons
    • Expressed Sequence Tags
    • Genes, Fungal
    • Genome, Fungal
    • methods: Genomics
    • Introns
    • genetics: Malate Dehydrogenase
    • Oligonucleotide Array Sequence Analysis
    • Research Support, Non-U.S. Gov't
    • Sequence Alignment

    Research Beacons, Institutes and Platforms

    • Manchester Institute of Biotechnology

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