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Originally published in Science Express on 13 January 2005
Science 25 February 2005:
Vol. 307. no. 5713, pp. 1321 - 1324
DOI: 10.1126/science.1103773
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Reports

The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans

Brendan J. Loftus,1* Eula Fung,2 Paola Roncaglia,3 Don Rowley,2 Paolo Amedeo,1 Dan Bruno,2 Jessica Vamathevan,1 Molly Miranda,2 Iain J. Anderson,1 James A. Fraser,4 Jonathan E. Allen,1 Ian E. Bosdet,5 Michael R. Brent,6 Readman Chiu,5 Tamara L. Doering,7 Maureen J. Donlin,8 Cletus A. D'Souza,9 Deborah S. Fox,4,10 Viktoriya Grinberg,1 Jianmin Fu,11 Marilyn Fukushima,2 Brian J. Haas,1 James C. Huang,4 Guilhem Janbon,12 Steven J. M. Jones,5 Hean L. Koo,1 Martin I. Krzywinski,5 June K. Kwon-Chung,13 Klaus B. Lengeler,4,14 Rama Maiti,1 Marco A. Marra,5 Robert E. Marra,4,15 Carrie A. Mathewson,5 Thomas G. Mitchell,4 Mihaela Pertea,1 Florenta R. Riggs,1 Steven L. Salzberg,1 Jacqueline E. Schein,5 Alla Shvartsbeyn,1 Heesun Shin,5 Martin Shumway,1 Charles A. Specht,16 Bernard B. Suh,17 Aaron Tenney,6 Terry R. Utterback,18 Brian L. Wickes,11 Jennifer R. Wortman,1 Natasja H. Wye,5 James W. Kronstad,9 Jennifer K. Lodge,8 Joseph Heitman,4 Ronald W. Davis,2 Claire M. Fraser,1 Richard W. Hyman2

Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its ~20-megabase genome, which contains ~6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.

1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
2 Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA.
3 Neurobiology Sector, International School for Advanced Studies (SISSA-ISAS), Via Beirut 2-4, 34014 Trieste, Italy.
4 Department of Molecular Genetics and Microbiology, Duke University Medical Center, 322 CARL Building, Research Drive, Box 3546, DUMC, Durham, NC 27710, USA.
5 Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.
6 Laboratory for Computational Genomics, Washington University, One Brookings Drive, St. Louis, MO 63130, USA.
7 Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
8 Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 S. Grand Boulevard, St. Louis, MO 63104, USA.
9 The Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada.
10 Research Institute for Children and the Department of Pediatrics, Louisiana State Health Science Center, Children's Hospital, 200 Henry Clay Avenue, New Orleans, LA 70118, USA.
11 University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
12 Unité de Mycologie Moléculaire, Institut Pasteur, 25 rue du Docteur Roux, Cedex 15, Paris, France.
13 Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institutes of Health (NIAID/NIH), 9000 Rockville Pike, Bethesda, MD 20892, USA.
14 Institut für Mikrobiologie, Heinrich-Heine-Universität, Universitätsstraße 1/26.12, Düsseldorf, Germany.
15 Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA.
16 Department of Medicine, Boston University, 650 Albany Street, EBRC-625, Boston, MA 02118, USA.
17 Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA.
18 18Joint Technology Center, J. Craig Venter Foundation, 5 Research Place, Rockville, MD 20850, USA.

* To whom correspondence should be addressed. E-mail: bjloftus{at}tigr.org

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