Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

James E. Galagan (), Sarah E. Calvo, Christina Cuomo, Li-Jun Ma, Jennifer R. Wortman, Serafim Batzoglou, Su-In Lee, Meray Baştürkmen, Christina C. Spevak, John Clutterbuck, Vladimir Kapitonov, Jerzy Jurka, Claudio Scazzocchio, Mark Farman, Jonathan Butler, Seth Purcell, Steve Harris, Gerhard H. Braus, Oliver Draht, Silke Busch, Christophe D'Enfert, Christiane Bouchier, Gustavo H. Goldman, Deborah Bell-Pedersen, Sam Griffiths-Jones, John H. Doonan, Jaehyuk Yu, Kay Vienken, Arnab Pain, Michael Freitag, Eric U. Selker, David B. Archer, Miguel Á. Peñalva, Berl R. Oakley, Michelle Momany, Toshihiro Tanaka, Toshitaka Kumagai, Kiyoshi Asai, Masayuki Machida, William C. Nierman, David W. Denning, Mark Caddick, Michael Hynes, Mathieu Paoletti, Reinhard Fischer, Bruce Miller, Paul Dyer, Matthew S. Sachs, Stephen A. Osmani and Bruce W. Birren
Additional contact information
James E. Galagan: The Broad Institute of MIT and Harvard
Sarah E. Calvo: The Broad Institute of MIT and Harvard
Christina Cuomo: The Broad Institute of MIT and Harvard
Li-Jun Ma: The Broad Institute of MIT and Harvard
Jennifer R. Wortman: The Institute for Genomic Research
Serafim Batzoglou: Stanford University
Su-In Lee: Stanford University
Meray Baştürkmen: Oregon Health & Science University
Christina C. Spevak: Oregon Health & Science University
John Clutterbuck: University of Glasgow
Vladimir Kapitonov: Genetic Information Research Institute
Jerzy Jurka: Genetic Information Research Institute
Claudio Scazzocchio: Université Paris-Sud, UMR8621
Mark Farman: Plant Science Building, 1405 Veteran's Drive, University of Kentucky
Jonathan Butler: The Broad Institute of MIT and Harvard
Seth Purcell: The Broad Institute of MIT and Harvard
Steve Harris: University of Nebraska
Gerhard H. Braus: Georg-August-University Gottingen
Oliver Draht: Georg-August-University Gottingen
Silke Busch: Georg-August-University Gottingen
Christophe D'Enfert: INRA USC 2019
Christiane Bouchier: Génopole-PF1
Gustavo H. Goldman: Universidade de Sao Paulo
Deborah Bell-Pedersen: Texas A&M University
Sam Griffiths-Jones: Wellcome Trust Genome Campus
John H. Doonan: John Innes Centre
Jaehyuk Yu: The University of Wisconsin-Madison
Kay Vienken: Max Planck Institute for terrestrial Microbiology
Arnab Pain: Wellcome Trust Genome Campus
Michael Freitag: University of Oregon
Eric U. Selker: University of Oregon
David B. Archer: University Park, University of Nottingham
Miguel Á. Peñalva: Consejo Superior de Investigaciones Científicas
Berl R. Oakley: The Ohio State University
Michelle Momany: The University of Georgia
Toshihiro Tanaka: National Institute of Technology and Evaluation (NITE)
Toshitaka Kumagai: National Institute of Advanced Industrial Science and Technology (AIST)
Kiyoshi Asai: National Institute of Advanced Industrial Science and Technology (AIST)
Masayuki Machida: National Institute of Advanced Industrial Science and Technology (AIST)
William C. Nierman: The Institute for Genomic Research
David W. Denning: The University of Manchester
Mark Caddick: Donnan Labs, The University of Liverpool
Michael Hynes: University of Melbourne
Mathieu Paoletti: University Park, University of Nottingham
Reinhard Fischer: Max Planck Institute for terrestrial Microbiology
Bruce Miller: University of Idaho
Paul Dyer: University Park, University of Nottingham
Matthew S. Sachs: Oregon Health & Science University
Stephen A. Osmani: The Ohio State University
Bruce W. Birren: The Broad Institute of MIT and Harvard

Nature, 2005, vol. 438, issue 7071, 1105-1115

Abstract: Abstract The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.

Date: 2005
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DOI: 10.1038/nature04341

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