About AspGD

AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species.

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New and Noteworthy

New look for AspGD website

We are pleased to announce that AspGD has been upgraded to a more streamlined look, with a new home page and improved navigation options. It may be necessary to clear cached pages and restart your web browser for the new pages to render properly. AspGD thanks Yuri Amatnieks for the beautiful color images, now displayed on the AspGD home page. AspGD welcomes your feedback. (Posted May 14, 2012)

AspGD Curation News
  • A. nidulans Genome Snapshot
  • A. fumigatus Genome Snapshot
  • A. niger Genome Snapshot
  • A. oryzae Genome Snapshot
  • New papers added to AspGD this week.
  • View Genome-wide Analysis papers in AspGD.
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    Intergenic Sequence Downloads
    AspGD provides two new methods for obtaining intergenic sequences. (1) From the locus summary page of any feature (click here for an example), click on the pull-down menu under "Retrieve Sequences" on the right side of the page, select "DNA plus flanking intergenic seq for...", and then click "View". (2) From the sequence download page for an organism in AspGD (click here for an example); the relevant download files end with "_orf_plus_intergenic.fasta.gz", which contain protein-coding genes plus intergenic regions or "_other_features_plus_intergenic.fasta.gz", which contain other genes (for example, non-coding RNAs) plus intergenic regions. In all cases, we provide the sequence of the feature itself plus sequence extending upstream and downstream to the boundary of the next transcribed feature (exclusive). For protein-coding genes that boundary is the start or stop codon, for non-coding RNAs it is the 5' or 3' end of the mature RNA. (Posted April 24, 2012)

    Improved Web Performance at AspGD
    We are pleased to announce that the AspGD website has a new server. We are excited about the new speed and responsiveness of the AspGD web pages as a result of our migration to a new Linux system. Our benchmark testing indicates that the new system processes web pages and tools, such as BLAST, approximately 3 times faster than our old server. We thank you for your patience during the down-time on Tuesday March 20, 2012, which was necessary to switch the database over to the new server. We hope you will enjoy the improved performance of the AspGD website. (Posted March 22, 2012)

    Updated Aspergillus fumigatus Af293 reference annotation
    The sequence of the A. fumigatus Af293 nuclear genome has been updated to the version at CADRE, which differs from the previous AspGD version in the number of undetermined ("N") nucleotides used to represent gaps between contigs on chromosomes II and IV.

    The structural annotation of each nuclear gene has been updated to the version contained in the CADRE set. New genes that are only present in the CADRE set have been added to AspGD. These genes have been assigned identifiers in the format Afu[chrom]g[number]. Genes that were present in the previous set at AspGD but which are not present in the CADRE set (i.e., genes deleted from the CADRE set) have now been deleted from the reference annotation, with the following exceptions, which have been retained:
    • Genes with an experimental description in AspGD
    • Genes with an ortholog or best hit in one or more of the other Aspergilli (excluding genes that have ONLY an ortholog or best hit annotated in the other A. fumigatus strain, A1163)
    • Genes with an ortholog or best hit in S. cerevisiae
    • Genes with annotated InterPro domain(s)
    • Genes with GO annotation in AspGD
    • tRNAs predicted by AspGD using tRNAscan-SE
    All untranslated region (UTR) sequences annotated in the CADRE gene set are included in the new reference annotation set.

    Mitochondrial genome sequence and annotation has been added. The sequence was generated by JCVI and the annotation was performed at the Broad Institute. Special thanks to Natalie Fedorova and Qiandong Zeng for the mitochondrial sequence and annotation, respectively. Mitochondrial gene identifiers have been assigned with the following format: AfuMt[number]. (Posted March 16, 2012)

    Archived News
    Click here to view archived news items.