Genome-wide single-nucleotide polymorphism map for Candida albicans

Abstract

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.

FIG. 1.

Flow chart for web-based development of SNP markers in C. albicans, with marker 1363/2056 used as an example. Two overlapping sequence contigs representing the two potentially heterozygous alleles for each genomic region were selected (A). Complete sequences for both contigs were then obtained (B) and compared by using the BLAST algorithm (C), followed by obtaining the actual sequence for overlapping parts of the contigs (D). The two sequences were aligned (E), heterozygous positions were identified, and forward and reverse primers flanking apparent SNPs were designed and synthesized. PCR simulations were performed (F), primer pairs were synthesized, and SNPs were confirmed by sequencing (G).

FIG. 2.

Whole-genome SNP map of C. albicans. Red stars, SNP markers that are heterozygous in strain SC5314; blue stars, SNP markers that are homozygous in strain SC5314. The numbers above the stars correspond to the numbering in Table S1 in the supplemental material. Based on the estimated sizes for C. albicans strain 1006 (obtained by pulsed-field gel electrophoresis), a map was created for the SfiI restriction sites of each chromosome (8). SfiI sites are indicated by vertical bars, and the names assigned by Chu et al. (8) are indicated within the boxes representing the chromosomes (e.g., 7A). The corresponding contig-19 sequences are shown along the lower side of each chromosome. Mapped genes from the fosmid map (http://alces.med.umn.edu/candida/) were used to order contig-19 sequences onto the map. When known, the directions (5′ to 3′) of contig-19 sequences are marked by arrows. Five contig-19 sequences on chromosome 1 have not been assigned to their corresponding SfiI fragments. They are located under chromosome 1 as a separate group (in brackets).

FIG. 3.

LOH detected in selected strains of C. albicans. (A) LOH in strain AF14 on chromosome fragment 1S. (B) LOH in strains RM1000, BWP17, AF12, and AF27 on chromosome fragment 1L. (C) LOH in strains RM1000, BWP17, AF12, and AF27 on chromosome fragment 5I. Arrows indicate LOH of SNP markers. Red stars, SNP markers that are heterozygous in strain SC5314; blue stars, SNP markers that are homozygous in strain SC5314.