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

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. [2012]) 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 1,133 features.

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)

Archived News

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