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
Upcoming Meetings & Courses
Gordon Research Conference on Cellular and Molecular Fungal Biology (CMFB)
Holderness, NH, USA
June 15-20, 2014
Molecular Mycology: Current Approaches to Fungal Pathogenesis
Woods Hole, MA, USA
June 16-30, 2014; Application Deadline: March 5
4th Central European Summer Course on Mycology and the 1st Rising Stars in Mycology Workshop
University of Szeged, Szeged, Hungary
July 4 – 11, 2014; Application Deadline: May 20
10th International Mycological Congress
August 3-8, 2014
New and Noteworthy
Sequence trace files available
We have added archival Aspergillus sequence data from the NCBI TraceDB site, and these data are now
available from our AspGD download site.
(Posted November 8, 2013)
AspGD Curation News
New "Big 4" ortholog alignment
We have added a new, streamlined, four-species protein alignment to the ortholog cluster pages in our Sybil
Comparative Genomics Viewer. This "Big 4" alignment displays a Clustal protein alignment of the orthologs from A.
nidulans FGSC A4, A. oryzae RIB40, A. fumigatus Af293 and A. niger CBS513.88 (see example). As we continue to add new species into our
Sybil Comparative Genomics Viewer, the number of proteins represented in each multispecies ortholog cluster has grown
significantly. We continue to provide an alignment of all of the orthologs from the full set of species, and now
include the "Big 4" alignment in addition. We hope this feature is helpful, and we welcome your feedback any time.
(Posted August 13, 2013)
A. niger annotation updates
The A. niger reference gene set has been updated, based on PASA analysis. 4,123 features were affected: 543 CDSs
were extended and 195 shortened; 30 features were merged into 15 features; 2,907 5-prime UTRs and 2,601 3-prime UTRs
were added or modified; New exons were added to the ends of 270 features, and the internal intron/exon structure was
modified for 491 features. The GBrowse Genome Browser displays the old annotation as a "Historic Track" to facilitate
visual comparison, for example, of new UTRs or gene model structure updates, for example, a gene merge. The current and historic reference annotation can be viewed alongside RNA-Seq
transcript data in AspGD JBrowse (zoom in to see spliced reads across intronic regions, including the intron within what was
previously annotated as an intergenic region).
(Posted August 13, 2013)
Introducing JBrowse for AspGD
JBrowse is now available for exploring large-scale data in AspGD, including RNA-Seq data for A. nidulans FGSC A4,
RNA-Seq and genomic variation data for A. fumigatus Af293, and RNA-Seq data for A. niger CBS 513.88 and A. oryzae
RIB40. To see the large-scale data in the region of any gene, select the JBrowse link on the Locus Summary page,
for example, in the "RNA-Seq Data" section of the A. nidulans veA page. The JBrowse software has been developed as part of the GMOD project.
The links to the GenomeView browser are no longer
displayed on the Locus Summary pages due to incompatibilities of the browser software software with some web browsers
and versions of Java. Genome View may still be accessed from the Search
Options page. (Posted June 19, 2013)
RNA-Seq data used to improve reference annotation for A. fumigatus
We have made significant updates to the structural annotation of the Aspergillus fumigatus Af293 reference
genome based on PASA analysis using RNA-Seq data
(from Müller et al. ) to provide experimental
support for gene model modifications. The coordinates of 5,174 features were updated: 1,044 CDSs were extended and
641 shortened; 28 features were merged into 14 features; 4,524 5-prime UTRs and 3,545 3-prime UTRs were added or
modified; New exons were added to the ends of 1,255 features, and the internal intron/exon structure was modified for
In addition, we have updated the structural annotation of the Aspergillus fumigatus A1163 (CEA10) strain, which
is not the reference strain, but for which we provide sequence files, protein domain files, and mulispecies BLAST
capabilities. The PASA analysis of A.
fumigatus A1163 utilized RNA-Seq data provided by JCVI (SRA project SRP003796).
(Posted April 2, 2013)
Click here to view archived news items.
AspGD Copyright © 2008-2013 The Board of
Trustees, Leland Stanford Junior University, and Broad Institute.
Permission to use
the information contained in this database was given by the
researchers/institutes who contributed or published the
information. Users of the database are solely responsible for
compliance with any copyright restrictions, including those applying to the author
abstracts. Documents from this server are provided "AS-IS" without any warranty,
expressed or implied.
To cite AspGD
please use the following
: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus
Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue)
How to cite AspGD.