Diverse lineages of Candida albicans live on old oaks. Illumina Sequencing of C. albicans Genomes

The human pathogen, Candida albicans, is considered an obligate commensal of animals, yet it is occasionally isolated from trees, shrubs and grass. We generated genome sequence data for three strains of C. albicans that we isolated from oak trees in an ancient wood-pasture, and compared these to the genomes of over 200 clinical strains. C. albicans strains from oak are similar to clinical C. albicans in that they are predominantly diploid and can become naturally homozygous at the mating locus through whole-chromosome loss of heterozygosity. Oak strains differed from clinical strains in showing slightly higher levels of heterozygosity genome-wide. Using phylogenomic analyses and in silico chromosome painting, we show that each oak strain is more closely related to strains from humans and other animals than to strains from other oaks. The genetic diversity of C. albicans from old oaks is not easily explained as contamination from a single animal source, and suggests they can live in this environment for extended periods of time.