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

Publication ,  Journal Article
Hu, G; Liu, I; Sham, A; Stajich, JE; Dietrich, FS; Kronstad, JW
Published in: Genome Biol
2008

BACKGROUND: Genome variability can have a profound influence on the virulence of pathogenic microbes. The availability of genome sequences for two strains of the AIDS-associated fungal pathogen Cryptococcus neoformans presented an opportunity to use comparative genome hybridization (CGH) to examine genome variability between strains of different mating type, molecular subtype, and ploidy. RESULTS: Initially, CGH was used to compare the approximately 100 kilobase MATa and MATalpha mating-type regions in serotype A and D strains to establish the relationship between the Log2 ratios of hybridization signals and sequence identity. Subsequently, we compared the genomes of the environmental isolate NIH433 (MATa) and the clinical isolate NIH12 (MATalpha) with a tiling array of the genome of the laboratory strain JEC21 derived from these strains. In this case, CGH identified putative recombination sites and the origins of specific segments of the JEC21 genome. Similarly, CGH analysis revealed marked variability in the genomes of strains representing the VNI, VNII, and VNB molecular subtypes of the A serotype, including disomy for chromosome 13 in two strains. Additionally, CGH identified differences in chromosome content between three strains with the hybrid AD serotype and revealed that chromosome 1 from the serotype A genome is preferentially retained in all three strains. CONCLUSION: The genomes of serotypes A, D, and AD strains exhibit extensive variation that spans the range from small differences (such as regions of divergence, deletion, or amplification) to the unexpected disomy for chromosome 13 in haploid strains and preferential retention of specific chromosomes in naturally occurring diploids.

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Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

2008

Volume

9

Issue

2

Start / End Page

R41

Location

England

Related Subject Headings

  • Virulence
  • Nucleic Acid Hybridization
  • Humans
  • Genome, Fungal
  • Genetic Variation
  • Cryptococcus neoformans
  • Cryptococcosis
  • Chromosomes, Fungal
  • Bioinformatics
  • Acquired Immunodeficiency Syndrome
 

Citation

APA
Chicago
ICMJE
MLA
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Hu, G., Liu, I., Sham, A., Stajich, J. E., Dietrich, F. S., & Kronstad, J. W. (2008). Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biol, 9(2), R41. https://doi.org/10.1186/gb-2008-9-2-r41
Hu, Guanggan, Iris Liu, Anita Sham, Jason E. Stajich, Fred S. Dietrich, and James W. Kronstad. “Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans.Genome Biol 9, no. 2 (2008): R41. https://doi.org/10.1186/gb-2008-9-2-r41.
Hu G, Liu I, Sham A, Stajich JE, Dietrich FS, Kronstad JW. Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biol. 2008;9(2):R41.
Hu, Guanggan, et al. “Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans.Genome Biol, vol. 9, no. 2, 2008, p. R41. Pubmed, doi:10.1186/gb-2008-9-2-r41.
Hu G, Liu I, Sham A, Stajich JE, Dietrich FS, Kronstad JW. Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biol. 2008;9(2):R41.

Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

2008

Volume

9

Issue

2

Start / End Page

R41

Location

England

Related Subject Headings

  • Virulence
  • Nucleic Acid Hybridization
  • Humans
  • Genome, Fungal
  • Genetic Variation
  • Cryptococcus neoformans
  • Cryptococcosis
  • Chromosomes, Fungal
  • Bioinformatics
  • Acquired Immunodeficiency Syndrome