Aspergillus nidulans Project Information

(also known as Emericella nidulans)

Contents

Additional information

Sequencing Project

The Aspergillus nidulans sequence project is part of the Broad Institute's Fungal Genome Initiative. Its goal is to release a 10X genome sequence coverage for Aspergillus nidulans, strain FGSC A4.

Our specific aims are as follows:

  1. Generate and assemble sequence reads yielding 10X coverage of the Aspergillus nidulans genome through whole genome shotgun sequencing.
  2. Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end long link information.
  3. Integrate the genomic sequence with existing physical and genetic map information.
  4. Perform automated annotation of the sequence assembly.
  5. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at Broad and by deposition of the sequence assembly in GenBank.

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/orders/). The resulting 13X assembly was made public March 2003, and the results of automated genome annotation will be made public in the spring 2003 releases. We overshot our sequence goal due to the coincidence with the switch to our new 3730 sequencing machines.

Oligonucleotide Array

In response to requests from the Aspergillus Genome Research Policy Committee (AGRPC), the National Institute of Allergy and Infectious Diseases funded the Pathogen Functional Genome Resource Center (PFGRC) to incorporate existing expression data into the Aspergillus nidulans genome annotation to improve gene calls and microarray design. PFGRC co-directors Scott Peterson and Robert Fleischmann, TIGR scientists Jennifer Wortman, Qiang(Charlie)Sun, Michael Holmes and visiting scientist Fangfang Pan (University of Georgia) participated in annotation improvement and oligo design. Gustavo Goldmann (Universidade de Sao Paulo) and Christophe d'Enfert (Institut Pasteur) furnished cDNA sequence information. Michelle Momany(AGRPC Chair, UGA) coordinated community input. The probe sequences have been mapped as features to the A. nidulans assembly. A file containing the sequences and the loci from which they were derived is available here.

Who are we?

The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

What is Aspergillus nidulans?

Aspergillus mutants
A. nidulans mutants. Courtesy of Ron Morris, University of Medicine and Dentistry of NJ

Significance

Aspergillus nidulans is one of the critical fungal systems in genetics and cell biology. It is important because it is closely related to a large number of other Aspergillus species of industrial and medical significance - e.g., A. niger, A. oryzae, A. flavus, and A. fumigatus - and serves as a model for understanding many biological questions. Unlike these other Aspergilli, which are asexual, A. nidulans has a well-characterized, conventional genetic system. Genes from other Aspergilli as well as some genes from mammalian species can function in A. nidulans through DNA-mediated transformation.

A. nidulans is a particularly useful model organism for studies of cell biology and gene regulation. The initial work on the genetics of tubulin and microtubules was done in A. nidulans. Similarly, A. nidulans contributes to our understanding of mitosis and the intracellular functions of the mitotic motors kinesin and cytoplasmic dynein. Carbon and nitrogen regulation are also well studied. One useful consequence of these regulatory studies is the characterization and development of the alcA alcohol dehydrogenase regulatable promoter, which is induced by alcohol and repressed by glucose, as a useful tool to control gene expression.

General Description

A. nidulans is a member of the ascomycetes. It grows rapidly as a filamentous fungus on solid or in liquid media under a variety of nutritional conditions. A. nidulans is homothallic, which means that any two strains can be mated directly. It is normally haploid, but can also be induced to grow as a heterokaryon or a vegetative diploid. It produces both asexual spores (conidia) and sexual spores (ascospores). It also undergoes development to produce at least nine different cell types.

Genome Facts

The size of the A. nidulans genome is approximately 31 Mb. It has 8 well-marked chromosomes containing an estimated 11,000-12,000 genes. About 900 genes have been identified in A. nidulans by conventional matings, 432 have been mapped to locus, and 254 are cloned and sequenced.