OutlineClick the species name for a description of the organism
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 Investigaciones Sanitarias.
An analysis of the A. fumigatus genome has been published by Nierman et al. (Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005, 438:1151-6) and a comparison of the A. fumigatus genome with those of A. oryzae and A. nidulans has been published by Galagan et al. (Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005, 438:1105-15).
Aspergillus fumigatus is the most frequently encountered opportunistic Aspergillus pathogen. A. fumigatus has been reported to be the major organism isolated from air samples, presumably because its spores are very small. The human infection caused by A. fumigatus is rated as the #2 health problem in the United States.
Aspergillus fumigatus is typically isolated from soil and is a saprophytic fungus that plays an essential role in recycling environmental carbon and nitrogen. Although A. fumigatus is not the most prevalent fungus in the world, it is one of the most ubiquitous of those with airborne conidia.
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).
Aspergillus clavatus is a close relative of A. fumigatus, the second most common fungal pathogen in the U.S. A. clavatus is only rarely pathogenic, although potently allergenic. A. clavatus can produce petulin, a substance which may be associated with disease in humans and other animals.
A. clavatus is found in soils and animal manure. It produces different cell types during development.
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).
Neosartorya fischeri (also known as Aspergillus fischeri, anamorph Aspergillus fischerianus) is a pathogenic fungus that can cause keratitis and possibly pulmonary aspergillosis in transplant patients, but is an extremely rare pathogen. Its inadequacy as a pathogen is interesting in light of its very close evolutionary relationship to A. fumigatus, the second most common fungal pathogen in the U.S., and so comparison of the A. fischerianus and A. fumigatus genomes should yield significant clues regarding A. fumigatus virulence and epidemiology. In addition, A. fischerianus has a known sexual cycle, so its comparison with its close asexual relative A. fumigatus may help elucidate why sexual reproduction is apparently absent in A. fumigatus. This would greatly advance A. fumigatus as an experimental system by facilitating genetic studies.
Neosartorya fischeri is found in soil, and its spores are found in agricultural products. It produces different cell types during development.
The Aspergillus niger genome (strain ATCC 1015) has been sequenced by JGI with funding provided by the Department of Energy (DOE). The strain chosen for sequencing (ATCC 1015) is also the wild type strain used in the first patented citric acid process nearly 90 years ago.
Aspergillus niger is an important industrial fungus that is widely used for the production of enzymes and metabolites, such as citric acid, but also as a host to produce heterologous proteins. Aspergillus niger has been used to study fungal protein secretion, proteolysis, cell wall biosynthesis, cell morphology and polarity, degradation of plant (cell wall) polysaccharides, central carbon metabolism and nutrient transport, both genetically and biochemically. Furthermore, as a soil saprobe with a wide array of hydrolytic and oxidative enzymes involved in the breakdown of plant lignocellulose, A. niger plays a significant role in the global carbon cycle. Finally, A. niger is an important model fungus for the study of eukaryotic protein secretion in general, the effects of various environmental factors on suppressing or triggering the export of various biomass degrading enzymes, molecular mechanisms critical to fermentation process development, and mechanisms involved in the control of fungal morphology.
Aspergillus niger is a common member of the microbial communities found in soils. The species is multinucleate and normally haploid, but can also grow as a heterokaryon or diploid. Conidia are normally mononucleate. Different cell types are formed as it undergoes development.
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.
An analysis of the A. oryzae genome has been published by Machida et al. (Genome sequencing and analysis of Aspergillus oryzae. Nature 2005, 438:1157-61) and a comparison of the A. oryzae genome with those of A. fumigatus and A. nidulans has been published by Galagan et al. (Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005, 438:1105-15).
Aspergillus oryzae is one of the filamentous fungi most widely used in fermentation industries in Japan. It is exploited in the production of sake, 'miso' (soybean paste), soy sauce, etc. and has been safely used for more than 1,000 years. It can also be used for large-scale production of enzymes and other proteins and is regarded as an ideal host for the synthesis of active proteins of eukaryotic origins that cannot be achieved with E. coli.
Aspergillus oryzae is predominantly isolated from soils, vegetative plant parts, seeds, and cotton fabrics.
The Aspergillus terreus sequencing project is part of the Broad Fungal Genome Initiative and is funded by the National Institute of Allergy and Infectious Disease (NIAID) through the Broad's Microbial Sequencing Center (MSC). Its goal is to release an annotated assembly with 10X genome sequence coverage for Aspergillus terreus strain NIH 2624. Dr. David Denning of the University of Manchester provided the genomic DNA for the sequencing project; the white paper including this organism was submitted by Bruce Birren (Broad Institute), David Denning (U. of Manchester), and Bill Nierman (TIGR).
Aspergillosis causes significant mortality and morbidity worldwide. Invasive aspergillosis is the leading infectious cause of death in leukemia and stem cell transplantation, affecting thousands of patients each year in the US alone. Aspergillus terreus, has emerged as a significant cause of aspergillosis, and infection caused by A. terreus carries a much higher mortality rate than any of the more than 20 pathogenic Aspergillus species, with mortality reaching 100% in many series. Importantly, A. terreus is completely resistant to amphotericin B, a crucial treatment for fungal infections. Aspergillus terreus is also the major source of lovastatin, the first drug of the ?statin? class to be approved by the FDA for the treatment of hypercholesterolemia in humans. The worldwide market for statins is more than $12 billion annually. In addition, lovastatin is a polyketide whose biosynthesis and regulation is likely relevant to that of other structurally related and commercially important molecules. In addition to lovastatin, A. terreus produces numerous other secondary metabolites (e.g., patulin, citrinin, isoterrin, asterriquinone) and commercially important enzymes (e.g., xylanase). Understanding the A. terreus genome and the differences between it and the genomes of carefully selected relatives will vastly improve our knowledge of pathogenesis, antibiotic resistance, and the biology of these infectious agents.
A. terreus is a filamentous ascomycete and is commonly found in soil. It grows well on either solid or liquid media and readily produces characteristic globe-shaped structures bearing asexual spores. In addition to producing typical Aspergillus aerial hyphae, A. terreus is unique among Aspergilli in producing lateral cells termed aleurospores in the absence of typical conidiophore structures in submerged culture. The presence of aleuorospores emphasizes the differences between the sequenced species, and could be of relevance in a clinical setting.
The Aspergillus flavus genome (strain NRRL 3357) has been sequenced by TIGR, with funding provided by the USDA.
Aspergillus flavus causes aspergillosis, a life-threatening human disease, particularly in patients who are immunosuppressed or have chronic lung disease. Aspergillus flavus is responsible for about 30% of the cases of aspergillosis. Aspergillus flavus also produces aflatoxin, the most important of the known mycotoxins. The fungus infests and produces aflatoxin on a variety of stored grains, including corn and other agricultural commodities. Aflatoxin, one of the most potent carcinogenic compounds known, causes liver cancer in humans. Annual economic losses for crops contaminated with aflatoxin is hundreds of millions of dollars. Because it produces aflatoxin, A. flavus is mutagenic, teratogenic, and acutely toxic to most animals and man. Aspergillus oryzae, a variant of A. flavus, is used in the fermentation of traditional Japanese beverages and sauces (e.g., soy sauce, sake, etc.). Apparently, commercial strains of A. oryzae do not produce aflatoxin.
Aspergillus flavus is an imperfect ascomycete that does not produce ascospores. It grows rapidly as a haploid filamentous fungus on solid or liquid media under a variety of nutritional conditions. It makes asexual spores but has no meiotic spore products. It is usually differentiated from other ascomycetes by its pattern of asexual spore production. A. flavus and A. oryzae appear to be variants of the same species.
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:
- Generate and assemble sequence reads yielding 10X coverage of the Aspergillus nidulans genome through whole genome shotgun sequencing.
- Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end long link information.
- Integrate the genomic sequence with existing physical and genetic map information.
- Perform automated annotation of the sequence assembly.
- 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.
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.
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.