Cryptococcus neoformans serotype A Genome Project

Project Information

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.

Sequencing Cryptococcus neoformans Serotype A

The Cryptococcus neoformans Serotype A H99 reference genome project was 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 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 the 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.

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.

Photo banner (top of home page) captions 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).

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).

Data access and citation

The genome assembly and annotation of strain H99 is available in Genbank under project accession PRJNA411. The genome is also available at FungiDb.

Data files formerly available on this website can be accessed on our fungal ftp site.

For use of this data, please cite:

Janbon G et al., "Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.", PLoS Genet, 2014 Apr 17;10(4):e1004261