CGH analysis of Candida albicans strains after in vitro evolution in the presence or absence of Fluconazole

Here we provide, for the first time, a longitudinal study of the prevalence, dynamics, and fixation of gross chromosomal rearrangements, including aneuploidy, in the presence and absence of fluconazole during a well-controlled in vitro evolution experiment. While no aneuploidy was detected in any of the no-drug control populations, in all fluconazole-treated populations analyzed, isochromosome 5L [i(5L)] appeared soon after drug exposure, was associated with increased fitness in the presence of drug, and became fixed in independent populations. In two separate cases, larger supernumerary chromosomes composed of i(5L) attached to other chromosome fragments appeared and were later lost during exposure to the drug. Other aneuploidies, particularly trisomies of the smaller chromosomes (Chr3-7), appeared throughout the evolution experiment, and the rapid accumulation of multiple aneuploid chromosomes per cell coincided with the highest resistance to fluconazole. All experimental strains were compared to the same reference control - sequenced strain SC5314. Some replicates are included and titled 'slide 2' for a given strain. Whole genomic DNA was used for all samples except the array labeled 'CHEFband' where we isolated DNA from a single CHEF gel band, labeled it, and hybridized it to the array.