Aspergillus Genetic Information
The 10th International Aspergillus Meeting (alias Asperfest10) is March 11-12, 2013, at Asilomar immediately before FGC27. Registration is online through the main FGC registration site workshops link http://www.fungalgenetics.org/2013/. Early registration and abstract submission deadlines are December 12.
This year in honor of a decade of Asperfest we will have a special LOGO CONTEST. More details will be sent out soon, but start those creative juices flowing.
pm - 6:00 pm Registration
Tuesday, March 12
Abstracts from the 9th Asperfest in Marburg Germany are available online.
Please welcome the following announcement from Liverpool:
We have performed whole transcriptome sequencing of A. nidulans using ABI's SOLiD high-throughput sequencing platform. Some preliminary data has been made publicly available for visualisation via the CADRE genome browser, with more to follow in the near future once we have overcome technical difficulties related to displaying large data sets. The dataset currently available was prepared from wild type A. nidulans (G00) grown for 16 hours in minimal media supplemented with nitrate a glucose. The library was prepared and sequenced in accordance with ABI's protocols for whole transcriptome RNA-seq, and the resulting reads aligned to the genome using Bowtie and Tophat.
To view the data go to cadre-genomes.org.uk and select A. nidulans. On the left of the page select "location view" then "configure this page". Our data is listed under "functional genomics" and can be added to the display.
Asperfest 9 will be held March 29-30, 2012 at the Max-Planck-Institute in Marburg, Germany, just before the ECFG11 meeting.
Registration will be organized by the ECFG website.
Aspergillus nidulans kinase knock-out mutant strains are available in arrayed sets.
News from the NCBI
Eight Aspergillus genomes have been reannotated with multi-genome Gnomon and the results presented in a poster at Asperfest 8. Two Aspergillus genomes with multi-genome Gnomon annotation are currently In RefSeq, Aspergillus niger CBS 513.88 (FGSC A513) (http://www.ncbi.nlm.nih.gov/genomeprj/19263 ) and Aspergillus oryzae RIB40 (http://www.ncbi.nlm.nih.gov/genomeprj/28175). For A. oryzae records in the nucleotide database please follow the link in the description at the bottom of the project. The gff file format and other formats are available for A. niger (ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_niger_CBS_513_88_uid19263/ ) and for A. oryzae (ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_oryzae_RIB40_uid28175/ ). If anybody is interested in the other Aspergillus Gnomon annotations please contact firstname.lastname@example.org with the following Subject heading: Aspergillus Gnomon annotation - attention Fungal Curator.
During the multi-genome Gnomon reannotation a possible contamination between Aspergillus flavus NRRL3357 and Neosartorya fischeri NRRL 181 was discovered which was then confirmed by JCVI and resulted in the removal (September 2010) of 2430 scaffolds in the A. flavus assembly ( see comment in http://www.ncbi.nlm.nih.gov/nuccore/AAIH00000000.2) and 538 scaffolds in the N. fischeri assembly ( see comments http://www.ncbi.nlm.nih.gov/nuccore/AAKE00000000 ). The removal involved small scaffolds and affected only 2 protein-coding genes for A. flavus and 11 protein-coding genes for N. fischeri.
Ronald deVries asked to post his presentation from the JGI genome workshop at the 26th Fungal Genetics Conference and the invitation to join the JGI Aspergillus genome project.
It is available here: DeVriesAspergillusJGIProject.pdf
The program for Asperfest 8 is now available. The complete program book with abstracts is also available for download.
A list of attendees is also available at the GSA site
Asperfest 8 will be Monday, March 14, 2011 (registration and evening poster reception) and Tuesday, March 15 (9AM-4PM) at Asilomar Conference Center immediately before the 26th Fungal Genetics Conference at Asilomar
Photos from the 2010 Asperfest 7 in the Netherlands
Please visit the
dedicated page for A. nidulans knock-out cassettes.
Knock- Out Cassettes for A. nidulans have been deposited at the FGSC
These cassettes were produced at Dartmouth Medical School and have been shipped to the FGSC as DNA suitable for transformation or amplification. We received two sets of 96 well plates. The first holds 60 ul of cassette DNA per well and the second holds mixed primers.
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:
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.
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
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 email@example.com with a tentative title and a brief description of your work (2-4 sentences).
Check out the new FGSC Strain and Plasmid catalog interfaces.
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.
All applications must be submitted through the Stanford jobs website.
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
Please see the updated Asperfest5 home page
January 11, 2008
Return to the FGSC home page