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Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.

Publication ,  Journal Article
Schein, JE; Tangen, KL; Chiu, R; Shin, H; Lengeler, KB; MacDonald, WK; Bosdet, I; Heitman, J; Jones, SJM; Marra, MA; Kronstad, JW
Published in: Genome Res
September 2002

The basidiomycete fungus Cryptococcus neoformans is an important opportunistic pathogen of humans that poses a significant threat to immunocompromised individuals. Isolates of C. neoformans are classified into serotypes (A, B, C, D, and AD) based on antigenic differences in the polysaccharide capsule that surrounds the fungal cells. Genomic and EST sequencing projects are underway for the serotype D strain JEC21 and the serotype A strain H99. As part of a genomics program for C. neoformans, we have constructed fingerprinted bacterial artificial chromosome (BAC) clone physical maps for strains H99 and JEC21 to support the genomic sequencing efforts and to provide an initial comparison of the two genomes. The BAC clones represented an estimated 10-fold redundant coverage of the genomes of each serotype and allowed the assembly of 20 contigs each for H99 and JEC21. We found that the genomes of the two strains are sufficiently distinct to prevent coassembly of the two maps when combined fingerprint data are used to construct contigs. Hybridization experiments placed 82 markers on the JEC21 map and 102 markers on the H99 map, enabling contigs to be linked with specific chromosomes identified by electrophoretic karyotyping. These markers revealed both extensive similarity in gene order (conservation of synteny) between JEC21 and H99 as well as examples of chromosomal rearrangements including inversions and translocations. Sequencing reads were generated from the ends of the BAC clones to allow correlation of genomic shotgun sequence data with physical map contigs. The BAC maps therefore represent a valuable resource for the generation, assembly, and finishing of the genomic sequence of both JEC21 and H99. The physical maps also serve as a link between map-based and sequence-based data, providing a powerful resource for continued genomic studies

Duke Scholars

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

September 2002

Volume

12

Issue

9

Start / End Page

1445 / 1453

Location

United States

Related Subject Headings

  • Serotyping
  • Sequence Analysis, DNA
  • Physical Chromosome Mapping
  • Karyotyping
  • Humans
  • Genome, Fungal
  • Genetic Markers
  • Electrophoresis
  • Databases, Genetic
  • DNA, Fungal
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Schein, J. E., Tangen, K. L., Chiu, R., Shin, H., Lengeler, K. B., MacDonald, W. K., … Kronstad, J. W. (2002). Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res, 12(9), 1445–1453. https://doi.org/10.1101/gr.81002
Schein, Jacqueline E., Kristin L. Tangen, Readman Chiu, Heesun Shin, Klaus B. Lengeler, William Kim MacDonald, Ian Bosdet, et al. “Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.Genome Res 12, no. 9 (September 2002): 1445–53. https://doi.org/10.1101/gr.81002.
Schein JE, Tangen KL, Chiu R, Shin H, Lengeler KB, MacDonald WK, et al. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 2002 Sep;12(9):1445–53.
Schein, Jacqueline E., et al. “Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.Genome Res, vol. 12, no. 9, Sept. 2002, pp. 1445–53. Pubmed, doi:10.1101/gr.81002.
Schein JE, Tangen KL, Chiu R, Shin H, Lengeler KB, MacDonald WK, Bosdet I, Heitman J, Jones SJM, Marra MA, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 2002 Sep;12(9):1445–1453.

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

September 2002

Volume

12

Issue

9

Start / End Page

1445 / 1453

Location

United States

Related Subject Headings

  • Serotyping
  • Sequence Analysis, DNA
  • Physical Chromosome Mapping
  • Karyotyping
  • Humans
  • Genome, Fungal
  • Genetic Markers
  • Electrophoresis
  • Databases, Genetic
  • DNA, Fungal