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United States Department of Agriculture

Agricultural Research Service

Research Project: ECOLOGICAL BASIS FOR AFLATOXIN REDUCTION THROUGH CROP MANAGEMENT AND BIOLOGICAL CONTROL

Location: Food and Feed Safety Research

Title: Genomic Islands in Pathogenic Filamentous Fungus Aspergillus fumigatus

Authors
item Fedorova, Natalie - THE J CRAIG VENTER INST
item Khaldi, Nora - UNIV OF DUBLIN IRELAND
item Joardar, Vinita - THE J CRAIG VENTER INST
item Maiti, Rama - THE J CRAIG VENTER INST
item Amedeo, Paolo - THE J CRAIG VENTER INST
item Anderson, Michael - UNIV OF MANCHESTER UK
item Crabtree, Jonathan - THE J CRAIG VENTER INST
item Silva, Joana -
item Badger, Jonathan - THE J CRAIG VENTER INST
item Albarraq, Ahmed - UNIV OF MANCHESTER UK
item Angiuoli, Sam -
item Bussey, Howard -
item Bowyer, Paul -
item Cotty, Peter
item Dyer, Paul -
item Egan, Amy -
item Galens, Kevin -
item Fraser-Liggett, Claire -
item Haas, Brian -
item Inman, Jason -
item Kent, Richard -
item Lemieux, Sebastien -
item Malavazi, Iran -
item Orvis, Joshua -
item Roemer, Terry -
item Ronning, Catherine -
item Sundaram, Jaideep -
item Sutton, Granger -
item Turner, Geoff -
item Venter, J. Craig -
item White, Owen -
item Whitty, Brett -
item Youngman, Phil -
item Wolfe, Kenneth -
item Goldman, Gustavo -
item Wortman, Jennifer -
item Jiang, Bo -
item Denning, David -
item Nierman, William -

Submitted to: PLoS Genetics
Publication Type: Review Article
Publication Acceptance Date: March 4, 2008
Publication Date: April 11, 2008
Citation: Fedorova, N.D., Khaldi, N., Joardar, V., Maiti, R., Amedeo, P., Anderson, M.J., Crabtree, J., Silva, J.C., Badger, J., Albarraq, A., Angiuoli, S., Bussey, H., Bowyer, P., Cotty, P.J., Dyer, P.S., Egan, A., Galens, K., Fraser-Liggett, C.M., Haas, B.J., Inman, J.M., Kent, R., Lemieux, S., Malavazi, I., Orvis, J., Roemer, T., Ronning, C.M., Sundaram, J.P., Sutton, G., Turner, G., Venter, J.C., White, O.R., Whitty, B.R., Youngman, P., Wolfe, K.H., Goldman, G.H., Wortman, J.R., Jiang, B., Denning, D.W., Nierman, W.C. 2008. Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus. PLoS Genetics. 4(4):e1000046:1-13

Technical Abstract: We present the genome sequences of a new clinical isolate, CEA10, of an important human pathogen, Aspergillus fumigatus, and two closely related, but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of CEA10 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and unique regions in each genome. While the core regions are 99.8% identical at the nucleotide level, identity over some variable regions can be as low 40%. Further comparison has revealed that A. fumigatus contains isolate- and species-specific genes, which comprise ~2% and 9% of the genome, respectively. These lineage-specific genes differ in variability, dispensability and size from the core genes and encode accessory functions. Subsequent phylogenetic analysis demonstrated that these genes emergence though duplication, accelerated diversification and/or gene loss (DDL). Most lineage-specific genes cluster in large chromosomal islands, which display a strong subtelomeric bias, have low gene density, and harbour a disproportionate number of pseudogenes, transposons and other repetitive elements. These regions may function as designated “gene dumps” and, simultaneously, as “gene factories”. Although A. fumigatus was chosen as the primary focus of this study, similar chromosomal structures were observed in the genomes of N. fischeri and A. clavatus, suggesting that all three species are poised for the rapid adaptation to heterogeneous environments such as soil, compost piles or a mammalian host.

Last Modified: 8/22/2014
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