1. The Institute for Genomic Research, Rockville, Maryland 20850, and The George Washington University School of Medicine, Department of Biochemistry and Molecular Biology, 2300 Eye Street NW, Washington DC 20037, USA
2. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
3. School of Medicine and Faculty of Life Sciences, The University of Manchester, Stopford Building, Manchester M13 9PT, UK
4. Departmento Microbiología II. Universidad Complutense de Madrid 28040, Spain
5. Tohoku University, 1-1 Tsutsumidori-Amamiyamachi Aoba-ku, Sendai 981-8555, Japan
6. School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, UK
7. Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118, USA
8. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
9. Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546-0312, USA
10. Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
11. Centro de Investigaciones Biológicas, CSIC, Madrid 28040, Spain
12. Departmento Microbiologia y Genetica, Universidad de Salamanca, 37007 Salamanca, Spain
13. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Brazil
14. Department of Molecular Biology, Innsbruck Medical University, A-6020 Innsbruck, Austria
15. Department of Plant Pathology, University of Wisconsin at Madison, Madison, Wisconsin 53706, USA
16. Department of Biotechnology, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
17. Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
18. Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
19. Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, Paris 75015, France
20. Unité des Aspergillus, Institut Pasteur, Paris 75015, France
21. Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
22. Departments of Microbiology, Molecular Biology and Biochemistry, Center for Reproductive Biology, University of Idaho, Moscow, Idaho 83844, USA
23. Department of Dermatology, Centre Hospitalier Universitaire Vaudois, CH-1011 Lausanne, Switzerland
24. Department of Bacteriology, Georg-August-University, D-37077 Gottingen, Germany
25. Tokyo University of Agriculture and Technology, Saiwai-chou 3-5-8, Fuchu, Tokyo 183-0054, Japan
26. Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, UK
27. Department of Food Microbiology and Toxicology, The University of Wisconsin, Madison, Wisconsin 53706, USA
28. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
29. Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
30. Present address: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA

Correspondence to: William C. Nierman¹ Correspondence and requests for materials should be addressed to W.N. (Email: wnierman@tigr.org). The genome sequence has been submitted to GenBank under the accession numbers NC_007194–NC_007201. All microarray expression data are available through ArrayExpress (http://www.ebi.ac.uk/arrayexpress) with accession numbers A-MEXP-205 (array design) and E-MEXP-332 and E-MEXP-333 (experimental data).

Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen^{1, 2, 3}. Its conidia production is prolific, and so human respiratory tract exposure is almost constant⁴. A. fumigatus is isolated from human habitats⁵ and vegetable compost heaps^{6, 7}. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis⁸. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.

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