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

Authors

James E. Galagan, Broad Institute of MIT and HarvardFollow
Sarah E. Calvo, Broad Institute of MIT and Harvard
Christina Cuomo, Broad Institute of MIT and Harvard
Li-Jun Ma, Broad Institute of MIT and Harvard
Jennifer R. Wortman, The Institute for Genomic Research, Rockville, MarylandFollow
Serafim Batzoglou, Stanford UniversityFollow
Su-In Lee, Stanford University
Meray Baştürkmen, Oregon Health & Science UniversityFollow
Christina C. Spevak, Oregon Health & Science University
Vladimir Kapitonov, Genetic Information Research Institute, Mountain View, CaliforniaFollow
Jerzy Jurka, Genetic Information Research Institute, Mountain View, CaliforniaFollow
Claudio Scazzocchio, Université Paris-Sud , France
Mark Farman, University of KentuckyFollow
Jonathan Butler, Broad Institute of MIT and Harvard
Seth Purcell, Broad Institute of MIT and Harvard
Steven D. Harris, University of Nebraska–LincolnFollow
Gerhard H. Braus, Georg-August-University Gottingen, GermanyFollow
Oliver Draht, Georg-August-University Gottingen, Germany
Silke Busch, Georg-August-University Gottingen, Germany
Christophe D'Enfert, Institut Pasteur, Paris, FranceFollow
Christiane Bouchier, Institut Pasteur, Paris, FranceFollow
Gustavo H. Goldman, Universidade de Sao Paulo, BrazilFollow
Deborah Bell-Pedersen, Texas A&M UniversityFollow
Sam Griffiths-Jones, The Wellcome Trust Sanger Institute, Hinxton, UK
John H. Doonan, John Innes Centre, Norwich, UK
Jaehyuk Yu, University of Wisconsin-MadisonFollow
Kay Vienken, University of Karlsruhe, Germany
Arnab Pain, The Wellcome Trust Sanger Institute, Hinxton, UK
Michael Freitag, Oregon State UniversityFollow
Eric U. Selker, University of OregonFollow
David B. Archer, University of Nottingham, UKFollow
Miguel Á. Peñalva, Consejo Superior de Investigaciones Científicas, Madrid, Spain
Berl R. Oakley, Ohio State UniversityFollow
Michelle Momany, University of GeorgiaFollow
Toshihiro Tanaka, National Institute of Technology and Evaluation, Tokyo, Japan
Toshitaka Kumagai, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
Kiyoshi Asai, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
Masayuki Machida, National Institute of Advanced Industrial Science and Technology, Tsukuba, JapanFollow
William C. Nierman, The Institute for Genomic Research, Rockville, MarylandFollow
David W. Denning, University of Manchester, UKFollow
Mark Caddick, University of Liverpool, UKFollow
Michael Hynes, University of Melbourne, AustraliaFollow
Mathieu Paoletti, University of Nottingham, UK
Reinhard Fischer, University of Karlsruhe, GermanyFollow
Bruce Miller, University of IdahoFollow
Paul Dyer, University of Nottingham, UKFollow
Matthew S. Sachs, Oregon Health & Science UniversityFollow
Stephen A. Osmani, Ohio State University
Bruce W. Birren, The Broad Institute of MIT and Harvard

Document Type

Article

Date of this Version

12-22-2005

Comments

Published in Nature 438 (December 22, 2005), pp. 1105-1115; doi 10.1038/nature04341 Copyright © 2005 Nature Publishing Group. Used by permission.

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.

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