title: Generation, annotation, and analysis of an extensive Aspergillus niger EST collection.
abstract: BACKGROUND
  Aspergillus niger, a saprophyte commonly found on decaying vegetation, is widely used and studied for industrial purposes. Despite its place as one of the most important organisms for commercial applications, the lack of available information about its genetic makeup limits research with this filamentous fungus.
  
  
  RESULTS
  We present here the analysis of 12,820 expressed sequence tags (ESTs) generated from A. niger cultured under seven different growth conditions. These ESTs identify about 5,108 genes of which 44.5% code for proteins sharing similarity (E < or = 1e(-5)) with GenBank entries of known function, 38% code for proteins that only share similarity with GenBank entries of unknown function and 17.5% encode proteins that do not have a GenBank homolog. Using the Gene Ontology hierarchy, we present a first classification of the A. niger proteins encoded by these genes and compare its protein repertoire with other well-studied fungal species. We have established a searchable web-based database that includes the EST and derived contig sequences and their annotation. Details about this project and access to the annotated A. niger database are available.
  
  
  CONCLUSIONS
  This EST collection and its annotation provide a significant resource for fundamental and applied research with A. niger. The gene set identified in this manuscript will be highly useful in the annotation of the genome sequence of A. niger, the genes described in the manuscript, especially those encoding hydrolytic enzymes will provide a valuable source for researchers interested in enzyme properties and applications.
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada. nsemova@gene.concordia.ca
authors.forename: Natalia
authors.initials: N
authors.lastname: Semova
authors.forename: Reginald
authors.initials: R
authors.lastname: Storms
authors.forename: Tricia
authors.initials: T
authors.lastname: John
authors.forename: Pascale
authors.initials: P
authors.lastname: Gaudet
authors.forename: Peter
authors.initials: P
authors.lastname: Ulycznyj
authors.forename: Xiang Jia
authors.initials: XJ
authors.lastname: Min
authors.forename: Jian
authors.initials: J
authors.lastname: Sun
authors.forename: Greg
authors.initials: G
authors.lastname: Butler
authors.forename: Adrian
authors.initials: A
authors.lastname: Tsang
mesh_terms: D001234:Aspergillus niger / Q000235:genetics*; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics*
chemical_list: D005656:Fungal Proteins