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Eukaryotic Cell, June 2004, p. 705-714, Vol. 3, No. 3
1535-9778/04/$08.00+0     DOI: 10.1128/EC.3.3.705-714.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans{dagger}

Anja Forche,1,2 P. T. Magee,1 B. B. Magee,1 and Georgiana May2*

Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455,1 Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 551082

Received 9 January 2004/ Accepted 4 March 2004

Single-nucleotide polymorphisms (SNPs) are essential tools for studying a variety of organismal properties and processes, such as recombination, chromosomal dynamics, and genome rearrangement. This paper describes the development of a genome-wide SNP map for Candida albicans to study mitotic recombination and chromosome loss. C. albicans is a diploid yeast which propagates primarily by clonal mitotic division. It is the leading fungal pathogen that causes infections in humans, ranging from mild superficial lesions in healthy individuals to severe, life-threatening diseases in patients with suppressed immune systems. The SNP map contains 150 marker sequences comprising 561 SNPs and 9 insertions-deletions. Of the 561 SNPs, 437 were transition events while 126 were transversion events, yielding a transition-to-transversion ratio of 3:1, as expected for a neutral accumulation of mutations. The average SNP frequency for our data set was 1 SNP per 83 bp. The map has one marker placed every 111 kb, on average, across the 16-Mb genome. For marker sequences located partially or completely within coding regions, most contained one or more nonsynonymous substitutions. Using the SNP markers, we identified a loss of heterozygosity over large chromosomal fragments in strains of C. albicans that are frequently used for gene manipulation experiments. The SNP map will be useful for understanding the role of heterozygosity and genome rearrangement in the response of C. albicans to host environments.

* Corresponding author. Mailing address: Department of Ecology, Evolution and Behavior, University of Minnesota, 1987 Upper Buford Circle, 100 Ecology, St. Paul, MN 55108. Phone: (612) 624-6737. Fax: (612) 624-6777. E-mail: gmay{at}tc.umn.edu.

{dagger} Supplemental material for this article may be found at http://ec.asm.org.

Eukaryotic Cell, June 2004, p. 705-714, Vol. 3, No. 3
1535-9778/04/$08.00+0     DOI: 10.1128/EC.3.3.705-714.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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