Aspergillus Genetic Information
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Past Asperfest Meetings/minutes
Additional Information
Protocols
Other protocols are available on the general methods page and on the Neurospora protocol page
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The preliminary program for Asperfest 7 is now available. (pdf)
Asperfest Poster submission is finished. The deadline was February 22, 2010.
1/4/10
We (David Denning, Bill Nierman and Natalie Fedorova) are about to launch the NIAID Genome Sequencing Center Contract project which we have titled “Community Resources for Aspergillus fumigatus.” The project will be accomplished over a two year period and we welcome your suggestions regarding possible future publications, story lines, focus, and associated analyses as well as specific genes or pathway that will be chosen for extensive manual annotation.
The project will have three components.
Component 1 is to sequence to high quality two additional reference genomes. These additional genomes will be AF10 and AF210 (both US strains from my time in the Stevens lab). We will likely use a combination of 454 paired-end reads and 100 bp Illumina reads. We are hoping that these sequencing platforms will give us a better view of the centromeres than we obtained using Sanger sequencing for Af293 and A1163, the other two sequenced reference strains. The relationship of these strains to others, by microsatellite typing, is described in our recent paper on azole resistance (Howard et al; Emerg Infect Dis, 2009).
Component 2 is to experimentally determine the gene models for A. fumigatus genes using RNA-seq from the Illumina platform. We will run RNAs from volunteer contributors for multiple conditions to see transcripts from nearly all of the A. fumigatus genes. We will use a pipeline at JCVI to process these reads to identify 5’ and 3’ UTRs, mRNA stop and start sites, intron/exon boundaries, and non-coding RNAs. The information will be incorporated into the annotated version of these four reference genome sequences.
There will be an opportunity for community folks to review and edit the annotation before the project is declared done.
Component 3 is to employ the Illumina sequencing platform to identify SNPs and INDELs from ~45 azole resistant clinical strains, and the original WT susceptible strains. The resultant data set will be available of to those who would like to participate in the analysis of this data. JCVI will provide informatics support for this analysis. These include strains from multiple patients from different locales, different resistance mutations, different decades and some are sequential isolates over time.
Those who have already volunteered to provide total RNAs for Component 2 are: Brian Wickes Elaine Bignell Scott Filler David Askew Nancy Keller Corné Klaassen Paul Bowyer Jüergen Löeffler
Fuller details about the strains and program will be posted shortly in the genome section of the Aspergillus website.
Natalie will be presenting a poster at AAA in Rome (assuming it is accepted) describing the project and possible novel analyses. We can discuss these at the meeting, or by e-mail. We do not intend to present, at least for publication, another 'genome paper', but rather focused papers on specific topics. We recognize that combined genomic and phenotypic/experimental data will generate more appropriate community interest than simply more genes and gene annotation.
12/4/09
Asperfest 7 will be March 28, 2010 (evening) and March 29, 2010 (full day) at the NH Conference Centre Leeuwenhorst in The Netherlands immediately before ECFG 10. The meeting will feature a variety of the best work in Aspergillus species. Get details on abstract submission and register online at: http://www.ecfg10.info/. Early registration for ECFG closes December 19, so don't delay.
Students: This year students have a special reduced registration rate
thanks to the generosity of
Steve Osmani and
Gustavo Goldman who donated royalties from their
Aspergillus
book for student support.
New Investigators: We will have a session this year featuring new investigators. If you have been an assistant professor or equivalent with your own group for 6 years or less, please email me at aspergillus@plantbio.uga.edu with a tentative title and a brief description of your work (2-4 sentences).
Programs from Asperfest-6 and other Aspergillus meetings can be found on our homepage. (http://www.fgsc.net/Aspergillus/asperghome.html). Check out the new FGSC Strain and Plasmid catalog interfaces.
The 2009 Aspergillus Bibliography is now available online as part of Fungal Genetics Reports, 56.
10/28/09
The final program
and minutes from AsperFest 6
are now available online as are several photos:
10/14/09
News from the AspGD Orthologs and syntenic regions 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 (please see this example). Alternatively, the ortholog clusters can be searched for gene name from any Aspergillus species, at http://aspgd.igs.umaryland.edu/. 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 comparative genome data (http://sybil.sf.net). 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.
January 2009
Scientific Curator All applications must be submitted through the Stanford jobs website.
Asperfest6 registration is available at the GSA webpage Online abstract submission is via the FGSC website.
September 29, 2008
Professor Herb Arst of Imperial College, London, will present the Pontecorvo Lecture at the 6th International Aspergillus Meeting.
September 15, 2008 Asperfest 6 will be held as a satellite meeting at the 25th Fungal
Genetics Conference at Asilomar.
March 11, 2008
The program and abstracts for the 5th International Aspergillus meeting are available online. Please see the updated Asperfest5 home page
January 11, 2008
January 2008 new strain update (pdf)
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