New and Noteworthy

The reference gene sets in AspGD have been updated, based on PASA analysis conducted by AspGD in 2015. The following changes were made:

• A. nidulans - 5 new features were added, and 4 former pseudogenes were reannotated as uncharachterized ORFs;
• A. fumigatus - 2,473 features were affected: 59 new features were added; the sequences for 242 features were extended and 154 shortened; 4 features were merged to create 2 new features; 1,757 5-prime UTRs and 1,333 3-prime UTRs were added or modified; terminal exons were added to 313 features; the intron/exon structure was modified for 389 features;
• A. niger - two new features were added (An11g02363 and An17g02286);
• A. oryzae - 7,279 features were affected: 287 new features were added; the sequences for 706 features were extended and 192 shortened; 192 features were merged to create 93 new feature; 5,141 5-prime UTRs and 5,213 3-prime UTRs were added or modified; terminal exons were added to 897 features; the intron/exon structure was modified for 500 features.

Please, visit the Chromosome History page to review the changes. (Posted September 15, 2015)

• 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.

As many of you may already be aware, the NIH R01 research grant that has supported development of the AspGD database will not be renewed … not because the NIH doesn't appreciate the value and importance of this resource to the Aspergillus research community, but because the current funding climate makes it difficult to support curation-intensive databases serving individual pathogens and relatively small research communities. However, NIH has provided one year of funding to ensure that information from AspGD is integrated into FungiDB, a component of the EuPathDB Bioinformatics Resource Center. We do not anticipate that AspGD will disappear: you should still be able to access the existing web site, at least for the foreseeable future, but curatorial engagement will have to be significantly reduced over the coming months.

The EuPathDB family of databases supports a wide range of microbial eukaryotes, including protozoan parasites and many fungal and oomycete species, including non-pathogens. This resource has been specifically designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information where available, along with comments and supporting evidence from the user community (PubMedIDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB also provides a variety of sophisticated tools for integrating and mining diverse Omics datasets, which we expect that Aspergillus researchers and other fungal biologists will find quite useful. See sidebar on the FungiDB web site for access to tutorials, videos, and exercises; more fungi-specific materials should become available over the coming months.

AspGD and FungiDB/EuPathDB will be working together to maximize value to the Aspergillus community, given the limited resources available. The upcoming AsperFest12 and 28th Fungal Genetics meetings in Asilomar (March 16-22, 2015) will be attended by staff from both groups, with presentations and a ‘help-desk’ to introduce the Aspergillus community to FungiDB. We look forward to productive discussions on how to ensure that Aspergillus researchers retain access to information from AspGD, learn to use FungiDB effectively and have a voice in its further development, and craft a strategy for meeting future informatics needs.

Jessica Kissinger (Univ Georgia) - Joint-PI, EuPathDB
Michelle Momany (Univ Georgia) - Community Liaison, AspGD & FungiDB
David Roos (Univ Pennsylvania) - Joint-PI, EuPathDB; Co-PI, FungiDB
Gavin Sherlock (Stanford Univ) - Principal Investigator, AspGD
Jason Stajich (UC Riverside) - Principal Investigator, FungiDB
Jennifer Wortman (Broad Inst) - Co-PI, AspGD

(Posted February, 2015)

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)

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)

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)

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)

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)

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