Cryptococcus neoformans var. grubii H99 Database

Cryptococcus neoformans var. grubii H99 (CNA3)

Cryptococcus neoformans is an opportunistic fungal pathogen that may cause meningitis in immunocompromised individuals. Often found in soils contaminated with bird feces, C. neoformans enters its host through the lungs via inhalation of spores. In healthy individuals the infection is usually controlled and asymptomatic, but in immunocompromised hosts the fungus can spread via the blood to infect the central nervous system and cause meningitis that is uniformly fatal if untreated. Few antifungal agents exist and drug-resistant strains are emerging.


Data site retirement

On 8/30/16 the Broad's Institute Cryptococcus database and web site will be retired due to expiration of funding. For many years we have been pleased to work closely with the Cryptococcus research community to create and support this resource. Please make plans to transition your analysis to other resources prior to 8/30/16.

C. neoformans, a member of the Basidiomycota phylum of the fungi, is more closely related to mushrooms than to ascomycete fungi like Saccharomyces cerevisiae or Candida albicans or filamentous fungi such as Neurospora crassa or Aspergillus nidulans.

The March 2013 release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a chromosome-based genome assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. Using RNA-seq from strand-specific and non-strand-specific libraries, we have updated the set of 6,962 predicted proteins in collaboration with Dr Guilhem Janbon at the Pasteur Institute. This work was supported by NIAID and by a grant from ANR (2010-BLAN-1620-01 program YeastIntrons) to GJ. A file mapping annotations between the current and previous versions may be downloaded here.

Sequencing Cryptococcus neoformans Serotype A

The Cryptococcus neoformans Serotype A sequencing project reflects a collaboration between the Fungal Genome Initiative at the Broad Institute and Fred Dietrich at the Duke Center for Genome Technology.

The Center for Genome Technology at Duke University Medical Center contributed ~2X coverage in plasmid reads. The Broad Institute of MIT and Harvard produced additional whole-genome shotgun sequence from 4 kb & 10 kb plasmids, 40 kb Fosmids and 110 kb BACs. The H99 BAC library was constructed by Klaus Lengeler and Joseph Heitman at Duke University, finger printed and end sequenced by Jim Kronstad and the Vancouver Genome Sequence Centre, and provided by these investigators to the Broad Institute. Genomic DNA for the H99 libraries was provided by James Fraser in the Heitman lab at Duke University. All the reads were assembled with Arachne.

cDNA was provided by Dr. Doris Kupfer at University of Oklahoma. RNA of samples for strand-specific library construction and sequencing were provided by Yuan Chen at Duke University

What is Cryptococcus neoformans?


Cryptococcus neoformans is an encapsulated fungal pathogen causing fatal meningitis in humans. The infection, initiated by inhalation into the lungs, occurs mainly in immunocompromised individuals, but can also occur in healthy individuals. Cryptococcus neoformans is usually found in tissues in the yeast form. Infection of the brain and meninges is the most common clinical manifestation. In immunocompetent individuals, the initial infection is usually controlled and asymptomatic and the organism remains dormant in a lymph node complex, much like tuberculosis. Reactivation occurs in immunocompromised hosts where the fungus can spread via the blood to infect the central nervous system. Once C. neoformans reaches this stage it can cause meningitis that is uniformly fatal if untreated. Few antifungal agents exist and drug-resistant strains are emerging.

There are four serotypes of C. neoformans. The serotype D was the first serotype chosen for sequencing studies at The Institute for Genome Research and Stanford Genome Technology Center because of its advanced genetic tools. However, more than 90% of clinical isolates and more than 99% of isolates from AIDS patients are of the more divergent serotype A strains. Sequencing a serotype A strain will increase our understanding of this disease and comparative studies between the serotypes A and D will help us define the genome structure and the development of pathogenicity.

General Description

Cryptococcus neoformans is unique among the most common human fungal pathogens in that it is a basidiomycete, thus it is evolutionarily divergent from the more common pathogenic ascomycetes (e.g., Candida albicans) and more closely related to wood rotting fungi (e.g., Phanerochaete chrysosporium), mushrooms (e.g., Coprinus cinereus), and plant pathogens (e.g., Ustilago maydis). Cryptococcus neoformans elaborates two specialized virulence factors, the polysaccharide capsule, which inhibits phagocytosis, and melanin, which serves as an antioxidant. The typical vegetative form of C. neoformans is the yeast form. The organism can also undergo sexual reproduction and form basidiospores. Sexual reproduction appears to occur much less frequently in nature than asexual or vegetative reproduction.

Genome Facts

Most isolates of C. neoformans are haploid. The size of the genome is approximately 19 Mb with 14 chromosomes. Cryptococcus neoformans has a defined sexual cycle involving mating between cells of the MATalpha and MATa types. Thus, classical genetic approaches can be applied to study this organism.

Home page images and credits

From left to right:

  • Encapsulated yeast cells
  • Sexual spores from Serotype A mating
  • Encapsulated yeast and sexual spores on defined media
  • Basidia head bearing four spores at distinct positions
  • Hyphae with a clamp cell, yeast cells and sexual spore chains

Source: Rajesh Velagapudi, and Joseph Heitman, M.D, PhD., Duke University

Scanning Electron Micrographs taken at "Center for Electron Microscopy" with the help of Valerie Knowlton (NCSU).

The phylogenetic tree was provided by Dr. Jason Stajich, UC Berkeley. For details please see "A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis" David A. Fitzpatrick, Mary E. Logue, Jason E. Stajich and Geraldine Butler. BMC Evolutionary Biology 2006, 6:99

Funding information

Funding support for genome sequencing of H99 was provided by the National Human Genome Research Institute, the National Institute of Allergy and Infectious Disease, and by the French National Research Agency (ANR) (2010-BLAN-1620-01 program YeastIntrons).