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Published online before print August 21, 2002, 10.1101/gr.81002
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Vol. 12, Issue 9, 1445-1453, September 2002

RESOURCES
Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans

Jacqueline E. Schein,1,4 Kristin L. Tangen,2,4 Readman Chiu,1 Heesun Shin,1 Klaus B. Lengeler,3 William Kim MacDonald,2 Ian Bosdet,1 Joseph Heitman,3 Steven J.M. Jones,1 Marco A. Marra,1 and James W. Kronstad2,5

1 Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada; 2 Biotechnology Laboratory, Department of Microbiology and Immunology, and Faculty of Agricultural Sciences, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; 3 Departments of Genetics, Pharmacology and Cancer Biology, and Microbiology and Medicine, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA

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.

[This paper is dedicated to the memory of Michael Smith, Founding Director of the Biotechnology Laboratory and the BC Cancer Agency Genome Sciences Centre. Supplemental material is available online at http://www.genome.org.]

4 These authors contributed equally to this work.

5 Corresponding author.

12:1445-1453 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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