Evolution of pathogenicity and sexual reproduction in eight Candida genomes

Geraldine Butler (), Matthew D. Rasmussen, Michael F. Lin, Manuel A. S. Santos, Sharadha Sakthikumar, Carol A. Munro, Esther Rheinbay, Manfred Grabherr, Anja Forche, Jennifer L. Reedy, Ino Agrafioti, Martha B. Arnaud, Steven Bates, Alistair J. P. Brown, Sascha Brunke, Maria C. Costanzo, David A. Fitzpatrick, Piet W. J. de Groot, David Harris, Lois L. Hoyer, Bernhard Hube, Frans M. Klis, Chinnappa Kodira, Nicola Lennard, Mary E. Logue, Ronny Martin, Aaron M. Neiman, Elissavet Nikolaou, Michael A. Quail, Janet Quinn, Maria C. Santos, Florian F. Schmitzberger, Gavin Sherlock, Prachi Shah, Kevin A. T. Silverstein, Marek S. Skrzypek, David Soll, Rodney Staggs, Ian Stansfield, Michael P. H. Stumpf, Peter E. Sudbery, Thyagarajan Srikantha, Qiandong Zeng, Judith Berman, Matthew Berriman, Joseph Heitman, Neil A. R. Gow, Michael C. Lorenz, Bruce W. Birren, Manolis Kellis () and Christina A. Cuomo ()
Additional contact information
Geraldine Butler: UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
Matthew D. Rasmussen: Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA
Michael F. Lin: Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA
Manuel A. S. Santos: University of Aveiro
Sharadha Sakthikumar: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Carol A. Munro: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
Esther Rheinbay: Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA
Manfred Grabherr: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Anja Forche: Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
Jennifer L. Reedy: Duke University Medical Center, Durham, North Carolina 27710, USA
Ino Agrafioti: Centre for Bioinformatics, Imperial College London, Wolfson Building, South Kensington, London SW7 2AY, UK
Martha B. Arnaud: Stanford University Medical School Stanford
Steven Bates: School of Biosciences, University of Exeter
Alistair J. P. Brown: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
Sascha Brunke: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute
Maria C. Costanzo: Stanford University Medical School Stanford
David A. Fitzpatrick: UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
Piet W. J. de Groot: Swammerdam Institute for Life Sciences, University of Amsterdam
David Harris: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Lois L. Hoyer: University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, USA
Bernhard Hube: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute
Frans M. Klis: Swammerdam Institute for Life Sciences, University of Amsterdam
Chinnappa Kodira: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nicola Lennard: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Mary E. Logue: UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
Ronny Martin: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute
Aaron M. Neiman: SUNY Stony Brook, Stony Brook, New York 11794, USA
Elissavet Nikolaou: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
Michael A. Quail: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Janet Quinn: Institute for Cell and Molecular Biosciences, Newcastle University
Maria C. Santos: University of Aveiro
Florian F. Schmitzberger: Stanford University Medical School Stanford
Gavin Sherlock: Stanford University Medical School Stanford
Prachi Shah: Stanford University Medical School Stanford
Kevin A. T. Silverstein: Biostatistics and Bioinformatics Group, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
Marek S. Skrzypek: Stanford University Medical School Stanford
David Soll: The University of Iowa, Iowa City, Iowa 52242, USA
Rodney Staggs: Biostatistics and Bioinformatics Group, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
Ian Stansfield: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
Michael P. H. Stumpf: Centre for Bioinformatics, Imperial College London, Wolfson Building, South Kensington, London SW7 2AY, UK
Peter E. Sudbery: University of Sheffield
Thyagarajan Srikantha: The University of Iowa, Iowa City, Iowa 52242, USA
Qiandong Zeng: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Judith Berman: Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
Matthew Berriman: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Joseph Heitman: Duke University Medical Center, Durham, North Carolina 27710, USA
Neil A. R. Gow: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
Michael C. Lorenz: The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
Bruce W. Birren: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Manolis Kellis: Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA
Christina A. Cuomo: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

Nature, 2009, vol. 459, issue 7247, 657-662

Abstract: Abstract Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/α2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.

Date: 2009
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DOI: 10.1038/nature08064

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