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Hu G
Liu I
Sham A
Stajich JE
Dietrich FS
Kronstad JW

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Hu G
Liu I
Sham A
Stajich JE
Dietrich FS
Kronstad JW
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Research

Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans

Guanggan Hu^*¹ , Iris Liu^*¹ , Anita Sham¹ , Jason E Stajich²^,3 , Fred S Dietrich² and James W Kronstad¹

¹Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada

²Department of Molecular Genetics and Microbiology, Institute for Genome Sciences and Policy, 287 CARL Building, Duke University Medical Center, Durham, NC 27710, USA

³Department of Plant and Microbial Biology, 121 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R41doi:10.1186/gb-2008-9-2-r41


Published:	22 February 2008

Subject areas: Genome studies, Medicine

Additional files

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.

Format: DOC Size: 98KB Download file

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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.

Format: DOC Size: 51KB Download file

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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.

Format: PPT Size: 467KB Download file

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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.

Format: DOC Size: 1.5MB Download file

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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.

Format: DOC Size: 68KB Download file

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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.

Format: DOC Size: 77KB Download file

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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.

Format: DOC Size: 1MB Download file

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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.

Format: DOC Size: 31KB Download file

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Additional data file 9:

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

Format: DOC Size: 2.1MB Download file

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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.

Format: DOC Size: 50KB Download file

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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.

Format: DOC Size: 690KB Download file

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Additional data file 12:

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

Format: DOC Size: 38KB Download file

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Additional data file 13:

Presented is a sample key for the CGH data.

Format: DOC Size: 32KB Download file

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Additional data file 14:

Presented is a tabulated list of primer sequences.

Format: DOC Size: 28KB Download file

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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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