Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans

Abstract

Previous analyses of diploid nuclear genotypes have concluded that recombination has occurred in populations of the yeast Candida albicans. To address the possibilities of clonality and recombination in an effectively haploid genome, we sequenced seven regions of mitochondrial DNA (mtDNA) in 45 strains of C. albicans from human immunodeficiency virus-positive patients in Toronto, Canada, and 3 standard reference isolates of C. albicans, CA, CAI4, and WO-1. Among a total of 2,553 nucleotides in the seven regions, 62 polymorphic nucleotide sites and seven indels defined nine distinct mtDNA haplotypes among the 48 strains. Five of these haplotypes occurred in more than one strain, indicating clonal proliferation of mtDNA. Phylogenetic analysis of mtDNA haplotypes resulted in one most-parsimonious tree. Most of the nucleotide sites undergoing parallel change in this tree were clustered in blocks that corresponded to sequenced regions. Because of the existence of these blocks, the apparent homoplasy can be attributed to infrequent, past genetic exchange and recombination between individuals and cannot be attributed to parallel mutation. Among strains sharing the same mtDNA haplotypes, multilocus nuclear genotypes were more similar than expected from a random comparison of nuclear DNA genotypes, suggesting that clonal proliferation of the mitochondrial genome was accompanied by clonal proliferation of the nuclear genome.

FIG. 1

Nucleotide substitutions and indels in the nine mtDNA haplotypes (Hap) of C. albicans. Numbers of strains sharing a haplotype are indicated in parentheses. Asterisks indicate nucleotide substitutions that are phylogenetically informative among mtDNA haplotypes. Since gaps (dashes) were not included in the phylogenetic analysis (see Fig. 2), they are not numbered as characters.

FIG. 2

(a) Single most-parsimonious tree of mtDNA haplotypes. Designations within circles represent strains listed by Cowen et al. (5). Numbers outside the circles represent mtDNA haplotype designations. Branch length is proportional to the number of character state changes (nucleotide substitutions), and scale is provided. (b) Same tree as that in panel a, except that reticulation is added as broken lines whose connections to branches are made with solid circles. The character numbers for the state changes (Fig. 1) associated with the reticulation in this tree appear on the broken lines. Although indels are not represented in this tree, only one (region 5, position 322 in the consensus sequence) showed reticulation, connecting haplotypes 4 and 7.

FIG. 2

(a) Single most-parsimonious tree of mtDNA haplotypes. Designations within circles represent strains listed by Cowen et al. (5). Numbers outside the circles represent mtDNA haplotype designations. Branch length is proportional to the number of character state changes (nucleotide substitutions), and scale is provided. (b) Same tree as that in panel a, except that reticulation is added as broken lines whose connections to branches are made with solid circles. The character numbers for the state changes (Fig. 1) associated with the reticulation in this tree appear on the broken lines. Although indels are not represented in this tree, only one (region 5, position 322 in the consensus sequence) showed reticulation, connecting haplotypes 4 and 7.

FIG. 3

Compatibility matrix of nucleotide substitutions that were phylogenetically informative among the nine mtDNA haplotypes of C. albicans. X, incompatible (i.e., all four possible combinations of 2 nucleotides at the two variable positions are present in Fig. 1); –, compatible (i.e., fewer than all four possible combinations of 2 nucleotides at the two variable positions are present in Fig. 1). Region 2 was not included because none of the polymorphisms in this region was phylogenetically informative among the haplotypes. (The variation in region 2 only distinguishes haplotype 3 from all of the rest. Therefore, sites in region 2 cannot be incompatible with sites in other regions.)

FIG. 4

UPGMA tree of similarity in nuclear DNA genotypes (5). The scale is the fraction dissimilar from zero to one. Boxes enclose distinct clusters of nuclear genotypes that also corresponded to mtDNA haplotypes. Asterisks designate strains of haplotypes 1 and 3 with exceptional nuclear genotypes.