This is the home of the Aspergillus Genome Database, a resource for genomic sequence data and gene and protein information for Aspergilli. AspGD is based on the Candida Genome Database and is funded by the National Institute of Allergy and Infectious Diseases at the US National Institutes of Health.

A. fumigatus isolates: 4 "reference" and 19 "target" Aspergillus fumigatus strains have been sequenced at the J. Craig Venter Institute (JCVI) using the Illumina platform. The list of sequenced strains includes (i) 7 drug resistant isolates, selected to facilitate the identification of new mechanisms of antifungal drug resistance (F series); and (ii) 12 genotypically linked isolates from 2 hospital outbreaks, included to validate the discriminatory power of existing genotyping markers (B series).

AspGD Locus summary pages (LSPs) for A. fumigatus genes contain a new Sequence Variation section (for example, see brlA), with links to short-read alignments displayed in the GenomeView browser, and to single nucleotide polymorphisms (SNPs) displayed in the GBrowse genome browser. The Sequence Variation section is located just below the Sequence Information section on each Locus Summary page.

To download the data, and for more information about the datasets themselves, please see our Large-Scale Datasets page. Files are available in VCF, BAM, and GFF format.

The SNPs displayed in GBrowse are defined relative to the Af293 reference sequence. We have added GBrowse tracks to display the SNPs observed in each sequenced strain individually, as well as a "SNP summary" track in which the color of the glyph indicates the relative frequency of the SNP; lighter blue color indicates that the SNP is observed in fewer strains and darker blue color indicates that the SNP is observed more frequently. The strains in which the SNP is observed are listed in the hover box displayed upon mouseover of a summary SNP glyph, along with the most common SNP nucleotide observed at this position. The polymorphism observed is displayed for each strain-specific SNP, and the associated quality score and read coverage is displayed in the hover box.

In the GenomeView browser, select the strains for which you would like to view short-read alignment data by clicking on the "eye" icon next to the strain name in the track list. You may browse by scrolling along the genome, zoom the view to see more or less detail, and navigate to specified positions in the genome or to individual genes (using the systematic gene name). General user documentation is available in the online GenomeView manual.

The A. fumigatus sequencing project at JCVI has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 and / or HHSN272200900007C. The sequence data were supplied to AspGD by Natalie Fedorova, JCVI. The GenomeView browser was developed at the Broad Institute, and GBrowse is a GMOD project. (Posted January 12, 2012)

• 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.

We are pleased to announce that we have now added A. oryzae information into AspGD. A. oryzae is the fourth Aspergillus species for which manually curated data are available in our database. The data loading is complete, and:

• A. oryzae RIB40 sequence is now available in all of the AspGD tools
• Each A. oryzae gene now has a Locus Summary page in the database
• A. oryzae genome and annotation is available in the GBrowse Genome Browser
• We have used tRNA-Scan to refine and update the A. oryzae tRNA predictions; like the protein-coding genes, the tRNA genes each have a Locus Summary page in the database
• Genes have been assigned predicted function, process, and localization annotations (Gene Ontology terms) based on orthology to S. cerevisiae, A. nidulans, A. fumigatus, and A. niger
• Additionally, protein-coding genes have been assigned predicted annotations based on protein motifs and domains (InterPro)
• We have added new bibliographies and topic areas for A. oryzae to our Highlights in Aspergillus biology page.
• Manual curation of the published scientific literature about A. oryzae genes is ongoing, and experimental data collected from the literature will continue to be added

We look forward to your feedback on the new A. oryzae species data in AspGD. (Posted November 21, 2011)

AspGD is pleased to announce that we have completed the manual curation of the gene-specific literature for A. niger and are further curating new literature as it becomes available. Because all of the available A. niger literature has been considered, we have now assigned Gene Ontology (GO) annotations to the root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" to gene products for which there are no experimental or computational data that would allow annotation with a non-unknown GO term. The evidence code for these "unknown" annotations, ND (No biological Data available), indicates that curators have searched for but have not found any relevant information as of the annotation date. AspGD is now "GO complete" for A. niger, meaning that each gene product has a GO annotation (including unknowns) in each of the three GO aspects. We look forward to your feedback on the new A. niger species data in AspGD. (Posted October 14, 2011)

We are pleased to announce that we have now added A. niger information into AspGD. The data loading is complete, and:

• A. niger CBS 513.88 sequence is now available in all of the AspGD tools
• Each A. niger gene now has a Locus Summary page in the database
• A. niger genome and annotation is available in the GBrowse Genome Browser
• We have used tRNA-Scan to refine and update the A. niger tRNA predictions; like the protein-coding genes, the tRNA genes each have a Locus Summary page in the database
• Genes have been assigned predicted function, process, and localization annotations (Gene Ontology terms) based on orthology to S. cerevisiae, A. nidulans, and A. fumigatus
• Additionally, protein-coding genes have been assigned predicted annotations based on protein motifs and domains (InterPro)
• Manual curation of the published scientific literature about A. niger genes is ongoing, and experimental data collected from the literature will continue to be added

We look forward to your feedback on the new A. niger species data in AspGD. (Posted August 23, 2011)

We have updated the annotation of A. nidulans and A. fumigatus tRNA genes, based on predictions using tRNAscan-SE and comparisons with S. cerevisiae homologs. Changes include assignment of several A. nidulans proline tRNAs that were initially predicted to be pseudogenes. In addition, tRNA names and aliases have been updated, as outlined in the AspGD Nomenclature Guide. (Posted July 25, 2011)

AspGD curators have compiled a set of references on a variety of topics relevant to Aspergillus biology. We have recently added new bibliographies and topic areas for A. fumigatus. The reference lists are intended to provide a brief overview of each subject area, including many key reviews, and to serve as a resource for those new to research in Aspergillus biology. (Posted July 19, 2011)

We have completed our curatorial review of the scientific literature about genes from A. nidulans and A. fumigatus, and would welcome you to review the information posted for the genes with which you are familiar. If there in any information that is inaccurate or incomplete, or if we are missing any references that should be cited, please let us know. We greatly appreciate your help in improving this community resource! (Posted July 18, 2011)

AspGD now has its own page on Facebook, where we will post occasional updates and announcements.
To see the AspGD posts in your Facebook news feed, you may "like" the page. (Posted July 8, 2011)

We have now added predictions about gene product function, role, and localization based on protein domains and motifs. Protein domains were determined using the InterProScan software from the European Bioinformatics Institute (EBI), and then domain-based Gene Ontology (GO) term assignments are made using the InterPro-to-GO mappings from GO Consortium web site. (Posted July 6, 2011)

We are pleased to announce that we have now fully integrated A. fumigatus information into AspGD. We have curated the entire published experimental literature that describes A. fumigatus genes, and have made extensive updates to the AspGD database and software to store and query information across multiple species simultaneously.

New and updated functionalities include:


• Each A. fumigatus Af293 gene has its own Locus Summary page in AspGD; see, for example, the A. fumigatus veA/Afu1g12490 Locus Summary page.


• The AspGD Locus Summary pages for each gene, in A. fumigatus as well as A. nidulans, contain a newly expanded section describing orthology within the Aspergilli, as well as orthologs in S. cerevisiae. Hyperlinks connect the AspGD Locus Summary pages between orthologous A. fumigatus and A. nidulans genes.


• We have curated the entire published experimental literature that describes A. fumigatus genes, and have written gene descriptions, compiled citation lists, assigned Gene Ontology (GO) terms, and collected mutant phenotypes for every characterized gene. We have also leveraged orthology with A. nidulans and S. cerevisiae to make predictions about the function, role, and localization of A. fumigatus genes that have characterized orthologs in these other species. All of this information is fully available on the AspGD web site and in the AspGD downloadable files.


• The sequence of the A. fumigatus Af293 genome is available in the AspGD searches.


• We have added predicted tRNA genes for A. fumigatus.


• We have implemented a multispecies BLAST tool, in which any subset of the multiple Aspergillus genomes can be selected and searched simultaneously.


• The AspGD Search tools, including the Quick Search, BLAST, Gene/Sequence search, Ortholog Search, and the Pattern Matching Tool, have all been updated to query multiple species.


• Quick Search results are now displayed in sections organized by species. Results that are not species-specific (e.g., individual GO terms, colleagues, references) are listed in a separate section on the results page.
  


• The Protein Information page (Protein tab) has been updated and reorganized to consolidate the information and links from the Protein Info, Domains/Motifs and Physiochemical Properties subtabs onto a single, more browseable page.


• Genome Snapshots are provided for both A. nidulans and for A. fumigatus, summarizing the status of the genome annotation on a daily basis.

We welcome your feedback on how we can improve the AspGD site and interface to make it more useful for your research. Please contact us any time. (Posted March 7, 2011)

Transposable element gene predictions were made at AspGD using TransposonPSI, an application based on PSI-BLAST similarity searches against a database of known transposons. You can use the AspGD Advanced Search tool to retrieve a list, by using the option to narrow your results to specific types of genes, and choosing the "transposable element gene" selection. (Posted October 15, 2010)

AspGD curators have reviewed all of the gene-specific literature for Aspergillus nidulans and are curating the new literature on an ongoing basis. Because all of the available A. nidulans literature has been considered, we have now assigned Gene Ontology (GO) annotations to the root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" to gene products for which there are no experimental or computational data that would allow annotation with a non-unknown GO term. The evidence code for these "unknown" annotations, ND (No biological Data available), indicates that curators have searched for but have not found any relevant information as of the annotation date. AspGD is now "GO complete" for A. nidulans, meaning that each gene product has a GO annotation (including unknowns) in each of the three GO aspects. (Posted October 1, 2010)

The AspGD Pattern Match tool now supports queries of the potential regulatory regions located between annotated features, in addition to the other chromosome- and feature-based sequence sets provided. To utilize this new feature, select "Intergenic regions" from the Sequence Database menu on the tool interface. You can search for specific sequence matches or for sequence patterns, using the character codes listed on the PatMatch tool page. (Posted September 1, 2010)

Each gene for which a knock-out cassette is available now has a "KO Cassette Available" link in the External Links section on its AspGD Locus Page (located just below the Sequence Information section). We have also added a link from the Phenotype Details page for each of these genes. The gene knock-out cassettes were produced at Dartmouth Medical School and have been shipped to the Fungal Genetics Stock Center (FGSC) as DNA suitable for transformation or amplification. More information about the resource is available on the FGSC web site, and a spreadsheet listing the cassettes and primers is available for download from the FGSC. (Posted August 20, 2010)

A new bibliography resource is now available at AspGD. Curators have compiled a set of references on a variety of topics relevant to Aspergillus nidulans biology. The reference lists are intended to provide a brief overview of each subject area, including many key reviews, and to serve as a resource for those new to research in Aspergillus biology. (Posted July 20, 2010)

AspGD now provides for download sequences from several Aspergillus and Aspergillus-related species and strains in addition to A. nidulans FGSC A4. The new additions include:

• Aspergillus clavatus NRLL 1
• Aspergillus flavus NRRL 3357
• Aspergillus fumigatus A1163
• Aspergillus fumigatus Af293
• Aspergillus niger ATCC 1015
• Aspergillus niger CBS 513.88
• Aspergillus oryzae RIB40/ATCC 42149
• Aspergillus terreus NIH2624
• Neosartorya fischeri NRLL 181

All sequences are available on the Sequence Downloads Page. See the Sequence Help Page for additional information. We will add additional strains and species as their genomic sequences become available. (Posted July 9, 2010)

We are pleased to announce the release of A. nidulans Annotation Version 5 in AspGD. This update merges the Version 4 annotation, which incorporates manually curated gene models from the Eurofung annotation, with a large set of updated gene model predictions from the Broad Institute. A more detailed description is found in the Version 5 release notes on the AspGD Sequence Documentation page. (Posted June 3, 2010)

We have added two new resource pages to the AspGD web site, and we welcome your help in improving them. The Methods & Protocols page is a place for links to papers that serve as useful references for laboratory techniques. The Images and Movies page is a collection of still images and movies for Aspergillus researchers. Both may be accessed using the links under "Community Resources" on the menu on the left-hand side of the home page. Please contact us if you have images or citations that you would like to contribute. (Posted April 22, 2010)

We have updated the sets of orthology mappings and predicted molecular function, biological process, and cellular location Gene Ontology annotations for A. nidulans genes. These assignments are based on the latest annotation at AspGD and at the Saccharomyces Genome Database (SGD).

The orthology mappings between A. nidulans and S. cerevisiae were made using the Inparanoid software developed at the Karolinska Institutet. In cases where an A. nidulans gene has an S. cerevisiae ortholog for which SGD has assigned GO terms, and these GO assignments meet our criteria (described in more detail in the associated README file), these GO terms are assigned to the A. nidulans gene with the evidence code "IEA" (Inferred from Electronic Annotation), which indicates that these annotations are predicted computationally, with no curatorial review. Downloadable files containing the orthology mappings and GO annotations are available. Based on orthology, we have inferred 10503 GO annotations for 2470 A. nidulans genes in AspGD. (Posted April 6, 2010)

AspGD now provides a BLAST tool to search multiple Aspergillus genomes at once. The genome sequences currently available are Aspergillus clavatus NRRL 1, Aspergillus flavus NRRL 3357, Aspergillus fumigatus A1163, Aspergillus fumigatus Af293, Aspergillus nidulans FGSC A4, Aspergillus niger ATCC 1015, Aspergillus niger CBS 513.88, Aspergillus oryzae RIB40/ATCC 42149, Aspergillus terreus NIH2624, and Neosartorya fischeri NRRL 181. We will add additional genomes as they become available. Try it out at the Multispecies Aspergillus BLAST page. (Posted March 19, 2010)

AspGD has expanded to include protein information for all verified and predicted ORFs. Using software and database tools developed at the Saccharomyces Genome Database (SGD), the Protein Information Pages display basic property, domain organization, structural and homology information. To view the page for a given protein, navigate to the Locus Summary page for the corresponding gene and click on the "Protein" tab towards the top of the page. Example Protein Pages: VeA; BenA; An8399. (Posted February 5, 2010)

The genome of Aspergillus fumigatus strain Af293 may now be explored using the GBrowse Genome Browser at AspGD. The Aspergillus fumigatus Af293 genome was sequenced by JCVI, the Sanger Institute, and the Institut Pasteur, and the sequence and annotation were downloaded from the Broad Institute Aspergillus download page. The tool may be accessed from the "A. fumigatus GBrowse" link on the menu located on the left-hand side of the AspGD home page. GBrowse allows you to zoom in or out on any genomic region or navigate to a different region of the chromosome, display restriction sites or G-C content, view DNA or protein sequence, or take advantage of additional browser features, which are described on the GBrowse Help Documentation page. Please note that you may need to select "Reset" (located under the search examples) to display all of the options the first time you view A. fumigatus GBrowse. The GBrowse software was written by Lincoln Stein as part of the Generic Model Organism Database (GMOD) Project. (Posted January 26, 2010)

We have added the pseudogenes and untranslated regions (UTRs) from version 4 of the A. nidulans annotation (the Eurofungbase annotation) to AspGD. The Advanced Search tool can be used to search and retrieve lists of pseudogenes and features with annotated UTR regions. (Posted December 16, 2009)

We have updated the sets of orthology mappings and predicted molecular function, biological process, and cellular location Gene Ontology annotations for A. nidulans genes. These assignments are based on the latest annotation at AspGD and at the Saccharomyces Genome Database (SGD).

The orthology mappings between A. nidulans and S. cerevisiae were made using the Inparanoid software developed at the Karolinska Institutet. In cases where an A. nidulans gene has an S. cerevisiae ortholog for which SGD has assigned GO terms, and these GO assignments meet our criteria (described in more detail in the associated README file), these GO terms are assigned to the A. nidulans gene with the evidence code "IEA" (Inferred from Electronic Annotation), which indicates that these annotations are predicted computationally, with no curatorial review. Downloadable files containing the orthology mappings and GO annotations are available. Based on orthology, we have inferred 13202 GO annotations for 3314 A. nidulans genes in AspGD. (Posted December 3, 2009)

The Aspergillus Genomic Online Community is a new group available to members of the worldwide community of Aspergillus researchers. The group is hosted by the Aspergillus Website, an information resource for Aspergillus and Aspergillosis. (Posted October 20, 2009)

A paper entitled "The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community" will appear in the 2010 Database Issue of Nucleic Acids Research. The paper is now available online as a Nucleic Acids Research Advance Access article. (Posted October 7, 2009)

AspGD users can now navigate from A. nidulans genes to orthologs and syntenic regions in the other sequenced Aspergillus species. Links are available from the Locus Summary page that navigate to an interactive comparative visualization tool (see example). Alternatively, the ortholog clusters can be searched for gene name from any Aspergillus species, at http://aspgd.broadinstitute.org/. Orthologs among the sequenced Aspergillus genomes were generated via a modified mutual best hit (MBH) approach, in which close paralogs are collapsed into a single node prior to MBH clustering.

AspGD is using Sybil, an open source, web-based software package for searching and visualizing the comparative genome data (http://sybil.sf.net). (Posted October 2, 2009)

The Broad Institute has released a reannotation of the Aspergillus nidulans genome sequence generated by an improved automated annotation pipeline. It is currently available on their website and is expected to appear in Genbank soon. AspGD is working to merge this annotation with the curated subset of the current annotation and we will post an update when the new release is available.

The previously published Eurofungbase reannotation of the Aspergillus nidulans genome (Wortman et al., 2009), the result of a community curation effort, is now available as Third Party Annotation (TPA) at Genbank through the efforts of the CADRE database. (Posted September 29, 2009)

We have generated orthology mappings between A. nidulans and A. fumigatus, and between S. cerevisiae and A. fumigatus, using the Inparanoid software developed at the Karolinska Institutet. The ortholog mapping files are available for download from our website.

We have also made Gene Ontology term predictions for A. fumigatus genes based on orthology to A. nidulans and S. cerevisiae. A file containing these predictions is also available for download from our website. In cases where an A. fumigatus gene has an A. nidulans ortholog for which we have GO terms in AspGD, or an S. cerevisiae ortholog for which the Saccharomyces Genome Database has assigned GO terms, and these GO assignments meet our criteria (described in more detail in the associated README file), these terms are assigned to the A. fumigatus gene with the evidence code "IEA" (Inferred from Electronic Annotation), which indicates that these annotations are predicted computationally, with no curatorial review. (Posted September 25, 2009)

We have now added tRNA-encoding genes to AspGD. These genes were predicted using the tRNAscan-SE algorithm developed by T. M. Lowe and S. R. Eddy. The names appear in the following format: a lower-case t (for "tRNA"), followed by the one-letter abbreviation of the amino acid with which it is charged, followed by the anticodon (in parenthesis) followed by an integer. For example, "tA(AGC)1" is an alanyl tRNA with an AGC anticodon.

The tRNAscan-SE algorithm predicts that there are 175 tRNA genes in the A. nidulans genome. The algorithm also predictes 5 pseudo-tRNA genes and they are noted as 'pseudogene' in the AspGD database. To find all of the tRNAs in AspGD, please use the Advanced Search tool or the following wildcard query for Quick Search: t*(*)*

These tRNA genes also appear in the GBrowse genome browser. (Posted August 26, 2009)

We are pleased to announce that AspGD is now available. The menu on the left-hand side of this page provides links to search options, tools, and additional information.

AspGD currently contains Locus Summary pages for 10,545 Aspergillus nidulans protein-coding genes that represent the most current sequence annotation, incorporating the original annotation from the Broad Institute, the re-annotation at TIGR, and the Eurofungbase community annotation effort. We have added 2,180 Gene Ontology (GO) term assignments for 968 genes, derived from the community curation effort involving Eurofungbase in conjunction with TIGR/JCVI and Aspergillus research laboratories. We have also predicted orthology to S. cerevisiae genes, using InParanoid, and have assigned 9,923 GO terms for 2,442 genes based on the current GO annotation of experimentally characterized S. cerevisiae orthologs in the Saccharomyces Genome Database (SGD). More than 1,400 publications have been added to AspGD and linked to the Literature Guides for the genes mentioned in their abstracts. Please note that because this initial reference load was based on automated PubMed searches, reference lists will be incomplete, and irrelevant references may be present. Going forward, references will be manually screened to ensure that each gene has a complete and accurate reference list.

Literature curation will be a major focus at AspGD in the coming months as we work towards comprehensive curation of gene function, localization, and mutant phenotype information from the A. nidulans literature. As an illustration of a manually curated Locus Summary page, we have collected and curated literature relevant to the veA gene.

Initially, we are concentrating on curation of A. nidulans, because it serves as a genetic model for the other Aspergilli, and it is the most well-represented of these species in the published experimental literature. In the future, we will add sequences from other Aspergillus species to AspGD and employ an optimized annotation pipeline across all genomes to maintain a set of current and consistent gene boundary annotations and link between genomes based on orthology and synteny data.

We welcome your comments and suggestions. Please feel free to contact us and let us know how we can better serve the Aspergillus research community. (Posted March 13, 2009)

We have submitted the following abstract to the 25th Fungal Genetics Conference, which will take place in March, 2009:

The Aspergillus Genome Database (AspGD), a curated database of Aspergillus gene, protein, and genomic sequence information for the fungal research community. Martha Arnaud¹, Gail Binkley¹, Marcus Chibucos², Maria Costanzo¹, Jonathan Crabtree², Stuart Miyasato¹, Prachi Shah¹, Marek Skrzypek¹, Jennifer Russo Wortman², and Gavin Sherlock<sup>1

1</sup>Department of Genetics, Stanford University, Stanford, CA 94305-5120 ²Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD

We have recently obtained funding to create a resource for the Aspergillus research community, AspGD, which will be a multispecies genomics database modeled on the Candida and Saccharyomyces Genome Databases. Our goal is to facilitate research on Aspergilli and on other medically and economically important fungal pathogens by providing a first-stop reference for Aspergillus genomics and molecular biology, with up-to-date, high-quality, curated scientific information and web-based research tools. We will implement an optimized annotation pipeline across all Aspergillus genomes, to maintain a set of current and consistent gene boundary annotations, and will incorporate links between genomes based on orthology and synteny data. Gene function, localization, and mutant phenotype annotations will be manually curated from the Aspergillus literature. We will provide web-based tools for sequence visualization and retrieval, and for analysis of sequence information and gene product annotations. All of the data in AspGD will be freely available to the public from http://www.aspgd.org/. In addition, we will maintain a colleague registry by which Aspergillus research community members may share contact information and research interests, to facilitate collaboration. We strive to be responsive to the needs of the research community, and we welcome your feedback and suggestions.

AspGD may be contacted from our Suggestions and Questions page. AspGD is supported by grant RO1 AI077599 from the NIAID at the NIH.

We hope to see you there! (Posted February 25, 2009)