Additional data file 1:

Presented is a table of Log2 ratios of divergent and conserved segments of the JEC21 genome relative to the genomes of the progenitor strains NIH12 and NIH433.

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Additional data file 2:

Presented is a table of the regions of putative recombination sites across all of the chromosomes in the JEC21 genome.

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Additional data file 3:

Presented is a figure of the variation in the genomes of strains representing the three molecular subtypes within the A serotype of C. neoformans.

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Additional data file 4:

Presented is a table of regions of difference in the genomes of four serotype A strains compared with the sequenced genome of strain H99.

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Additional data file 5:

Presented is a table of the quantitative RT-PCR analysis of gene copy number relative to the H99 genome.

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Additional data file 6:

Presented is a table of the quantitative RT-PCR analysis of gene copy number relative to the JEC21 genome.

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Additional data file 7:

Presented is a figure showing the replacement of a gene on chromosome 13 to examine copy number.

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Additional data file 8:

Presented is a document describing the genomic hybridization analysis of transformants carrying a replacement at the APT1 gene on chromosome 13 in strains H99, CBS7779, and WM626. This file also presents an estimation of relative copy number by quantitative real-time PCR of selected markers on chromosome 13 in strains H99, JEC21, CBS7779, and WM626.

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Additional data file 9:

Presented is a figure showing the phenotypic differences between strains H99, CBS7779, and WM626.

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Additional data file 10:

Presented is a table of the average Log2 ratios of the chromosomes in three AD hybrid strains upon hybridization to the tiling arrays of the JEC21 and H99 genomes.

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Additional data file 11:

Presented is a figure showing an RFLP-PCR analysis of the origin of chromosome 1 in 16 AD hybrid strains.

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Additional data file 12:

Presented is a tabulated list of Cryptococcus neoformans and C. gattii strains.

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Additional data file 13:

Presented is a sample key for the CGH data.

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Additional data file 14:

Presented is a tabulated list of primer sequences.

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Additional data file 15:

Presented are the figure legends for the figures presented in Additional data files 3, 7, 9 and 11.

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