Progress 12/01/03 to 11/30/07
Outputs
OUTPUTS: Aspergillus flavus is a competitive saprobe, a plant pathogen, and an animal pathogen. In addition, it produces aflatoxin, one of the most potent naturally occurring carcinogens. A whole genome-sequencing project was initiated with the goal of better understanding the factors that allow this fungus to be such a successful saprobe and pathogen. Sequencing was conducted at The Institute of Genomic Research (J. Craig Venter Institute) using a multiple library strategy to attain maximal genome coverage and linkage of the assembled contigs. A combination of 3-4 kb and 10 kb insert size libraries and a 50 kb linking library was employed. Annotation tools were trained on genomic sequence of A. oryzae as well as A. flavus and A. oryzae ESTs. A web-based browser was developed that allows Blast matches to genes, proteins and genomic sequence of other Aspergillus species, alignments of ESTs, and GO annotations. New annotations are posted on the site. Sequence reads can be obtained from
NCBI. Links to the web browser and to other information on the sequencing project can be found at: www.aspergillusflavus.org. As part of an outreach program supported by the grant, a high school teacher was funded to develop a project entitled, Bioinformatics and Genomics in the High School Biology Curriculum.
PARTICIPANTS: PI: Gary A. Payne and Ralph A. Dean Technician: G.R. OBrian Collaborators: Bhatnagar, D (USDA/ARS/SRRC);Yu, J.(USDA/ARS/SRRC);Cleveland, T. E.(USDA/ARS/SRRC); Nierman, W (JCVI);Machida, M. (Japan; Woloshuk, C. P.(Purdue University) Robertson, D.(North Carolina State University) Traning or professional development: Georgianna, D.R., Graduate student; Smith, C. A.,graduate student; Pritchard, B.L., Post graduate training.
Impacts
The genome of A. flavus was assembled into 79 scaffolds ranging in size from 4.5 Mb to 1.0 Kb. Over 75% of the genome is represented in the 10 largest scaffolds. The newly sequenced genome of A. flavus allowed a genomic comparison with A. oryzae, a closely related fungus that does not produce aflatoxins and has lost the ability to infect plants, animals and humans. By comparative genomics we have shown that these two fungi are very similar. The estimated genome size of 36.8 Mb for A. flavus is similar to that for A. oryzae (36.7). Further, these two fungi have a similar number of nonribosomal peptide synthases and polyketide synthases, the two major multifunctional enzymes involved in secondary metabolism. One striking difference between the two fungi is a translocation in A. flavus between chromosomes 2 and 6. In addition, the sequenced strains of these fungi have approximately 300 genes unique to each species. Further comparative analysis of this fungus with the other
sequenced species of Aspergillus will allow a better understanding of genes involved in pathogenicity, secondary metabolism, and mycotoxin production. Finally, findings from these studies will have broad implications for understanding the Aspergillus genus as a whole.
Publications
- Payne, G.A., Nierman, W.C., Wortman, J.R., Pritchard, B.L., Brown, D. Dean, R.A., Bhatnagar, D., Cleveland, T.E., Machida, M. and Yu, J.J. 2006. Whole genome comparison of Aspergillus flavus and A. oryzae. Medical Mycology. 44:S9-S11.
- Payne, G. A. 2008. Genomics of Aspergillus flavus. In, The Aspergilli: Genomics, Medical Applications, Biotechnology, and Research Methods. Editors, Osmoni and Goldman CRC Press. Mycology Series, volume 26.
- Smith, C. A., Woloshuk, C. P., Robertson, D. and Payne, G. A. 2007. Silencing of the Aflatoxin Gene Cluster in a Diploid Strain of Aspergillus flavus is Suppressed by Ectopic aflR Expression. Genetics 179:1-10.
|
Progress 10/01/04 to 09/30/05
Outputs
Aspergillus flavus is a pathogen of maize, peanuts, cottonseed, and tree nuts, and contaminates them with the carcinogen, aflatoxin. There are no effective control procedures for the fungus. To gain a greater understanding of the factors responsible for pathogenicity and aflatoxin production, a whole genome sequencing project for Aspergillus flavus was initiated in 2003. The sequencing project is near completion and we are now in the manual annotation and comparative genomics phase. Sequencing to 5-X coverage was done at The Institute of Genomic Research (TIGR) under the supervision of Dr. William Nierman. A multiple library strategy with different insert sizes was used to attain maximal genome coverage and maximal linkage of the assembled contigs. A combination of 3-4 kb and 10 kb insert size libraries and a 50 kb linking library were used. The sequence reads can be obtained from NCBI. Automated annotation was done under the supervision of Dr. Jennifer Wortman at
TIGR using annotation tools trained on genomic sequence of A. oryzae as well as A. flavus and A. oryzae ESTs. Dr. Jiujiang Yu at the USDA/ARS/SRRC directed the sequencing of the A. flavus ESTs, which have been critical to gene annotation. Fine finishing of the sequence, which includes closing the small gaps is near completion. A web browser was developed at North Carolina State University allows Blast matches to genes, proteins and genomic sequence of other Aspergillus species, alignments of ESTs, and GO annotations. New annotations will be updated on the site. Links to the web browser and to other information on the sequencing project can be found at www.aspergillusflavus.org. The genome has been assembled into 79 scaffolds ranging in size from 4.5 Mb to 1.0 Kb. Over 75 percent of the genome is represented in the 10 largest scaffolds. The estimated genome size of 36.3 Mb is similar to that for A. oryzae (36.8 Mb), a closely related species. These two fungi are enriched in genes for
secondary metabolism. A. flavus, for example, is predicted to have 34 polyketide synthases, 22 non-ribosome peptide synthases, 77 ABC transporters and 122 cytochrome p450 enzymes.
Impacts
Aspergillus flavus and A. oryzae (the predominate fungus used in food fermentation) are closely related and are likely ecotypes. A comparison of the genomes of these two fungi will likely reveal information on changes that have occurred during the domestication of A. oryzae, and help identify pathogenicity factors in A. flavus.
Publications
- Price, M. S., Conners, S. B., Tachdjian, S., Kelly, R. M. and Payne, G. A. 2005. Nutritional and environmental factors trigger diverse gene expression profiles for aflatoxin associated genes. Fungal Genetics and Biology 42:506-518.
- Price, M. S., Yu, J.J., Nierman, W.C., Kim, H.S., Pritchard, B.A., Bhatnagar, D., Cleveland, T.E. and Payne, G.A. 2005. The aflatoxin pathway regulator AflR induces gene transcription inside and outside of the aflatoxin biosynthetic cluster. FEMS (In Press)
|
Progress 10/01/03 to 09/30/04
Outputs
Aspergillus flavus is a widely distributed filamentous fungus that normally occurs as a saprophyte in the soil or on decaying organic matter. It is pathogenic to plants, insects and animals and produces aflatoxin, one of the most toxic and carcinogenic naturally occurring compounds. A. flavus is also the second leading cause of aspergillosis in humans. A whole genome sequencing project funded by the USDA/NRI and USDA/ARS and conducted at TIGR is nearing completion. Preliminary studies of the 33.1 Mb draft sequence, which consists of 17 scaffolds representing 2995 contigs, indicate that the genome contains approximately 13,800 genes. Thus the A. flavus genome appears to be larger than either A. nidulans or A. fumigatus. Aspergillus species are of interest in part because of the large range of clinically and industrially important secondary metabolites they synthesize. An initial scan of the A. flavus genome for proteins involved in the production of these secondary
metabolites revealed the presence of 24 putative polyketide synthases and 25 putative non-ribosomal peptide synthases. Manual annotation and analysis of the genome is being coordinated through North Carolina State University and will be made available at www.Aspergillusflavus.org.
Impacts
An available complete genome sequence of A. flavus will greatly facilitate progress in understanding the ecology and evolutionary biology of the fungus, the regulatory networks controlling fungal development and primary and secondary metabolism.
Publications
- Payne, G. A., Dean, R. A. Yu, J., Bhatnagar, D., Cleveland, T. E. and Nierman, W. C. The Aspergillus flavus sequencing project. European Conference on Fungal Genetics, March 2004. Copenhagen, Denmark.
|
|