Resources
Outline
Broad-Sequenced Genomes
Aspergillus nidulans
Monsanto is collaborating in this effort by contributing their assembly, which represents ~3X genomic coverage, to the public. These data consist of 16,144 contigs that cover 29,123,109 bp.
Broad Institute produced additional whole genome shotgun sequence from 4kb & 10kb plasmids, 40kb Fosmids and 110kb BACs and assembled these data together with Monsanto's reads. The genomic DNA was provided by Berl R. Oakley at the Ohio State University. The BAC library was provided by Ralph Dean at North Carolina State University and is available at Clemson University Genomics Institute (https://www.genome.clemson.edu/cgi-bin/orders/).
6,300 unique ESTs were provided by Rolf Prade and Bruce Roe at Oklahoma State University.
Aspergillus terreus
Dr. David Denning of the University of Manchester provided the genomic DNA for the A. terreus sequencing project.
Other Genomes
Aspergillus fumigatus
The Aspergillus fumigatus genome (strain Af293) has been sequenced through joint effort by TIGR, the Sanger Centre, and the Institute Pasteur with major funding provided by the National Institute of Allergy and Infectious Diseases (NIAID), the Wellcome Trust and the Fondo de Investigationes Sanitarias. The assembly is also available from GenBank with accession AAHF00000000.
Aspergillus clavatus
The Aspergillus clavatus genome (strain NRRL 1) has been sequenced by TIGR with funding provided by the National Institute of Allergy and Infectious Diseases (NIAID). The assembly is available from GenBank with accession AAKD03000000.
Neosartorya fischeri
The Neosartorya fischeri genome (strain NRRL 181) has been sequenced by TIGR with funding provided by the National Institute of Allergy and Infectious Diseases (NIAID). The assembly is available from GenBank with accession AAKE00000000.
Aspergillus niger
The Aspergillus niger genome (strain ATCC 1015) has been sequenced by JGI with funding provided by the Department of Energy (DOE). Information on the genome is available at http://genome.jgi-psf.org/Aspni1/Aspni1.home.html.
Aspergillus oryzae
The Aspergillus oryzae genome (strain RIB40 / ATCC 42149) has been sequenced by the National Institute of Technology and Evaluation (NITE) in collaboration with the National Institute of Advanced Industrial Science and Technology (AIST) and other members of the A. oryzae Genome Analysis Consortium. Information on this genome is available at http://www.bio.nite.go.jp/ngac/e/rib40-e.html.
Tools
Gene Prediction Tools
The following gene prediction tools were used in preparing annotations of A. nidulans, A. terreus, and A. flavus:
Other Computational Tools
These tools were also used in preparing the data for this website.
- Multiple alignments of gene families were prepared using MUSCLE. (Reference: Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
- Whole-genome alignments used in the Synteny Map and Dot Plot were prepared using PatternHunter.
- HMMER was used to annotation protein domains on predicted genes.
- NCBI BLAST was used to identify regions homologous to protein sequences in NCBI's NR database.
- BLAT was used to align ESTs to the A. nidulans and A. terreus genomes.