Diverse lineages ofCandida albicanslive on old oaks

Abstract

AbstractThe human pathogen,Candida albicans, is considered an obligate commensal of animals, yet it is occasionally isolated from trees, shrubs and grass. We generated deep genome sequence data for three strains ofC. albicansthat we isolated from oak trees in an ancient wood-pasture, and compared these to the genomes of the type strain and 21 other clinical strains.C. albicansstrains from oak are similar to clinicalC. albicansin that they are predominantly diploid and can become naturally homozygous at the mating locus through whole-chromosome loss of heterozygosity (LOH). LOH regions in all genomes arose recently suggesting that LOH mutations usually occur transiently inC. albicanspopulations. Oak strains differed from clinical strains in showing less LOH, and higher levels of heterozygosity genome-wide. Using phylogenomic analyses,in silicochromosome painting, and comparisons with thousands moreC. albicansstrains at seven loci, we show that each oak strain is more closely related to strains from humans and other animals than to strains from other oaks. Therefore, the isolation ofC. albicansfrom oak is not easily explained as contamination from a single animal source. The high heterozygosity of oak strains could arise as a result of reduced mitotic recombination in asexual lineages, recent parasexual reproduction or because of natural selection. Regardless of mechanism, the diversity ofC. albicanson oaks implies that they have lived in this environment long enough for genetic differences from clinical strains to arise.