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.

Conclusion: 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.

Figure 1

Virtual normalization and direct subtraction. A) Relative signal intensity of clones, determined as a ratio of the signal intensity of each individual clone versus the maximum signal intensity present on the array. Signal intensities for the colonies derived from a single 384 well microplate are displayed as a function of relative colony signal strength. B) Proportion of unique ESTs obtained at various stages of the gene discovery process. 1: Sequencing of the first 192 randomly selected clones, 2: Sequencing of the last 192 clones of the 1920 randomly selected clones. 3: Sequencing of the first 192 clones obtained by virtual normalization. 4: Sequencing of the last 192 clones from the 2,304 clones obtained by virtual subtraction. 5: Sequencing of the first 192 clones selected after virtual normalization and direct subtraction, first round. 6: Sequencing of the last 192 clones selected after both virtual normalization and direct subtraction, first round. 7: Sequencing of the first 192 clones selected after virtual normalization and direct subtraction, second round. 8: Sequencing of the last 192 clones from the 10,738 clones selected after virtual normalization and direct subtraction, second round.

Figure 2

GO mappings for the A. niger proteins. Relative representation of GO mappings for the proteins coded for by the unique set of A. niger singletons and contigs. A) Biological process; B) Cellular component; C) Molecular function. Note, because individual proteins can map to multiple GO categories, the sum of the GO mappings can exceed 100%.