Coccidioides Genomes

Project Information

Coccidioides immitis is a soil fungus which causes coccidioidomycosis, also known as "valley fever," a serious and sometimes fatal disease in otherwise healthy people. C. immitis was placed on a NIAID group II list of priority emerging and re-emerging pathogens. Coccidioides species have also become models for studying the evolutionary biology of pathogenic fungi.

The Coccidioides immitis sequence project targeted multiple Coccidioides strains and was supported by both NHGRI and NIAID through the Broad Institute's Fungal Genome Initiative and its Microbial Sequencing Center (MSC).

Under the Coccidioides sequence project, the genome of the RS strain was finished and anntated. An additional 11 strains of Coccidioides and EST libraries from both species (C. immitis and C. posadasii) were sequenced. Strains targeted for sequencing were selected by the Coccidioides Genome Resources Consortium (CGRC) and include:

  Strain Pop.* Seq Strain notes gDNA provider
C. immitis RS CC Finish   Theo Kirkland & Suganya Viriyakosol
H538.4 CC 3X endospore cluster phenotype; less pathogenic than RS Garry Cole & Ruth Schaller
RMSCC 2394 SCNM 8X geographic type John Galgiani
RMSCC 3703 SCNM 3X phylogenetic position John Galgiani
C. posadasii RMSCC 2133 TSA 8X geographic type John Galgiani
RMSCC 3700 TSA 3X extreme low virulence in mice John Galgiani
RMSCC 3488 SCM 8X geographic type John Galgiani
RMSCC 1038 SCM 3X extreme low virulence in mice John Galgiani
Silveira A 5X enhanced virulence in mice; most widely reported experimental strain John Galgiani
RMSCC 1040 A 3X enhanced virulence in mice John Galgiani
RMSCC 1037 A 3X enhanced virulence in mice John Galgiani
CPA 0001 A 3X recent environmental isolate exhibiting virulence in murine model Marc Orbach
CPA 0020 A 3X recent environmental isolate exhibiting virulence in murine model Marc Orbach
CPA 0066 A 3X recent environmental isolate exhibiting virulence in murine model Marc Orbach

*Populations: A=Arizona, CC=Central California, SCNM=Southern California/Northern Mexico, SCM=Southern/Central Mexico, TSA=Texas, South America

SAGE data were generously provided by Marc Orbach, John Galgiani, M. Alejandra Mandel, and Ellen M. Kellner.

What is Coccidioides?

Coccidioides immitis is an ascomycete soil fungus found in the Central Valley of California, San Diego and Baja California. It is one of a pair of species (the other being C. posadasii) found in the desert regions of North America, Mexico, and scattered areas in South America, particularly Argentina, that causes coccidioidomycosis, also known as "valley fever." In the soil, both Coccidioides species produce hyphae and mitospores, and both are specifically adapted to live in mammals, including humans. When mitospores are inhaled, they enlarge to make spherules, which divide internally to make endospores. One spherule can release thousands of endospores, which, in turn, mature into spherules. No sex is known in either species.

C. immitis and the closely related C. posadasii are ascomycete fungi found in the desert regions of North America, Mexico, and South America that cause coccidioidomycosis, or valley fever. These two fungi are responsible for nearly all cases of Valley Fever in the United States, and C. immitis has been placed on the 2003 NIAID group II list of priority emerging and re-emerging pathogens [1]. C. posadasii is not included on the NIAID list as legislation that classified C. immitis as a bioterrorism organism was generated prior to the discovery that Coccidioides comprised two genetically distinct species.

Coccidioides spp. cause serious and sometimes fatal disease in otherwise healthy people of all ages and ethnicity. On average, 100,000 persons are infected per year in the United States alone [2, 3]. Approximately 35% of these are symptomatic, and some illnesses last months before resolving [4]. Approximately 5% of infections require medical therapy and some of these infections are fatal [4]. In Arizona alone there was an 8-fold increase in the number of coccidioidomycosis hospitalizations from 1998 to 2001 [5]. Recent data also indicates a substantial impact on the health of college students in the state of Arizona [6]. Infections in older people are more likely to require hospitalization or be fatal [7], and the rate of serious infection in immunocompromised individuals (e.g., people on chemotherapy and with transplants) is substantial [7]. In Arizona, nearly 30% of all reported pneumonia cases are due to Coccidioides. There is also evidence of a genetic disposition to disease dissemination particularly among African Americans and Filipinos [8]. This disposition is independent of socioeconomic or environmental factors [8] and is of particular interest to the US Military as a large percentage of its troops are members of these ethnic groups [9]. When Coccidioides spreads beyond the lungs, it frequently goes to the bones, joints, skin, and brain. Brain infection (meningitis) is lethal if not treated, while bone and skin infection can persist for life. The incidence of this disease is increasing due to both increased spore exposure as a consequence of new development and population growth in the Southwest, especially California and Arizona [4, 7, 10], and growth of the immune-compromised population [7, 10].

On the evolutionary front, C. posadasii and C. immitis have become models for studying the evolutionary biology of pathogenic fungi. Over 200 strains of the two species from across the Western Hemisphere have been typed at nine microsatellite loci, more than for any other fungal species [11]. Most of the strains are from C. posadasii due to its greater geographic range.


NIAID. List of NIAID Emerging and Re-emerging Diseases 2003. 2005 [cited 2005 03/18/05];
Chiller, T.M., J.N. Galgiani, and D.A. Stevens, Coccidioidomycosis. Infectious Disease Clinics Of North America, 2003. 17(1): p. 41-+.
Stevens, D.A., Coccidioidomycosis. New England Journal Of Medicine, 1995. 332(16): p. 1077-1082.
Hector, R.F. and R. Laniado-Laborin, Coccidioidomycosis-A Fungal Disease of the Americas. PLoS Med, 2005. 2(1): p. e2.
Galgiani, J.N., personal communication. 2005.
Orbach, M., personal communication. 2005.
Kirkland, T.N. and J. Fierer, Coccidioidomycosis: a reemerging infectious disease. Emerg Infect Dis, 1996. 2(3): p. 192-9.
Pappagianis, D., et al., Ethnic-Background And The Clinical Course Of Coccidioidomycosis. American Review Of Respiratory Disease, 1979. 120(4): p. 959-961.
Olivere, J.W., et al., Coccidioidomycosis - the airborne assault continues: An unusual presentation with a review of the history, epidemiology, and military relevance. Aviation Space And Environmental Medicine, 1999. 70(8): p. 790-796.
Cole, G.T., et al., A vaccine against coccidioidomycosis is justified and attainable. Medical Mycology, 2004. 42(3): p. 189-216.
Taylor, J.W. and M.C. Fisher, Fungal multilocus sequence typing - it's not just for bacteria. Current Opinion In Microbiology, 2003. 6(4): p. 351-356.

This sequencing project was supported by the National Institute of Allergy and Infectious Disease, National Institutes of Health funded Genome Sequencing Center for Infectious Diseases at the Broad Institute.

Data access and citation

The  sequences and annotation of these Coccidioides genomes are available in Genbank, under accessions AAEC03000000, AASO01000000, AATX01000000, ABBC01000000, ABAI01000000, ABBB01000000, ABFM01000000, ABFN01000000, ABFO01000000, ABIS01000000, ABIT01000000, ABIU01000000, ABIV01000000, and ABIW01000000.

For use of this data, please cite:

Sharpton TJ et al., "Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.", Genome Res, 2009 Aug 28;19(10):1722-31.

Neafsey D et al., "Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control." Genome Res, 2010. 20: 938-946 .