The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

Abstract

The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu.

Figure 1.

Locus Summary page. The Locus Summary page is the hub around which all of the AspGD gene information is organized. This example shows the classes of data that are summarized on the page: names and aliases, the gene description, orthologs and best hits, GO annotations, phenotypes, sequence information, community annotation displayed in the locus summary notes section and the references from which the names and description have been curated. Tabs and hyperlinks access additional information and details, including the Locus History page, which explains any sequence and annotation changes affecting the gene; the Literature Guide page, which has a comprehensive listing of references that pertain to the gene; the full set of GO and phenotype annotations; and the GBrowse genome browser.

Figure 2.

Statistics of GO term annotation for A. nidulans in AspGD. Red bars represent the number of A. nidulans genes at AspGD that are annotated to each of the selected GO slim terms based on published literature (annotated directly to each term itself, or annotated to one of its more granular child terms). Blue bars represent the number of A. nidulans genes annotated to each GO slim term based on predictions made from the annotation of orthologous, characterized S. cerevisiae genes at the SGD. As of 6 August 2009, AspGD contains a total of 14 804 GO annotations for 3297 unique genes.

Figure 3.

Comparative analysis and refinement of gene models. Comparative alignments of orthologous proteins from 10 Aspergillus genomes, shown in the Sybil viewer. (A) Structural rearrangement among Aspergillus genomes (here A. nidulans and A. niger CBS 513.88 are emphasized). (B) Presence or absence of introns and different numbers of exons. (C) Gene duplications (paralogs) in one species relative to other species. (D) Intron structure, such as inordinately long introns relative to orthologs in other species. (E) Gene deletion (or creation) in syntenic blocks among species. Differences in structural annotation among species that can be illuminated with the Sybil view, thus leading to refinement of gene models, include missed gene calls, gene truncations, failure to predict small exons and incorrect intron predictions leading to spurious exons or gene merges.