Figure 3 .

Extensive chromosome loss in C. neoformans AD hybrid isolates. Genomic DNA of the AD hybrid isolate and the control (equal amount of genomic DNA of H99 and JEC21) were competitively hybridized to 70-mer oligonucleotide probes designed from the JEC21 and H99 genomes. The serotype-specific probes on the array slide were determined on the basis of bioinformatic analysis of the probe sequences against the H99 and JEC21 genomic sequences (see Materials and methods section). The hybridization signal of serotype-specific probes was analyzed by the use of GenePix and GeneSpring software to produce the log2 ratio of R635/R532 (AD hybrid/control) value and plotted in Microsoft Excel. Each block of different color represents a chromosome. For the serotype D genome, from left to right the 14 blocks match chromosomes 1 to 14. Serotype A chromosome numbers are redefined according to the corresponding serotype D chromosome (for the corresponding serotype A and D chromosomes, see Figure S1). Each triangle represents a serotype-specific probe. The line in each block (chromosome) represents the average log2 ratio of genomic hybridization. Average log2 ratios lower and higher than 0.5 reflect chromosome loss and duplication, respectively. For example, strain IUM92-6198 lost serotype D Chr 9, and serotype A Chr 3, Chr5, Chr 8, and Chr 11. Strain AD2-71 has partial loss of serotype A Chr 1, Chr 2, and Chr 3.