RT Journal
A1 Sharpton, Thomas J.
A1 Stajich, Jason E.
A1 Rounsley, Steven D.
A1 Gardner, Malcolm J.
A1 Wortman, Jennifer R.
A1 Jordar, Vinita S.
A1 Maiti, Rama
A1 Kodira, Chinnappa D.
A1 Neafsey, Daniel E.
A1 Zeng, Qiandong
A1 Hung, Chiung-Yu
A1 McMahan, Cody
A1 Muszewska, Anna
A1 Grynberg, Marcin
A1 Mandel, M. Alejandra
A1 Kellner, Ellen M.
A1 Barker, Bridget M.
A1 Galgiani, John N.
A1 Orbach, Marc J.
A1 Kirkland, Theo N.
A1 Cole, Garry T.
A1 Henn, Matthew R.
A1 Birren, Bruce W.
A1 Taylor, John W.
T1 Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
JF Genome Research 
JO Genome Research 
YR 2009 
FD October 01 
VO 19 
IS 10 
SP 1722 
OP 1731 
DO 10.1101/gr.087551.108 
UL http://genome.cshlp.org/content/19/10/1722.abstract 
AB While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including humans. Infection results from environmental exposure to Coccidiodies, which is believed to grow as a soil saprophyte in arid deserts. To investigate hypotheses about the life history and evolution of Coccidioides, the genomes of several Onygenales, including C. immitis and C. posadasii; a close, nonpathogenic relative, Uncinocarpus reesii; and a more diverged pathogenic fungus, Histoplasma capsulatum, were sequenced and compared with those of 13 more distantly related Ascomycetes. This analysis identified increases and decreases in gene family size associated with a host/substrate shift from plants to animals in the Onygenales. In addition, comparison among Onygenales genomes revealed evolutionary changes in Coccidioides that may underlie its infectious phenotype, the identification of which may facilitate improved treatment and prevention of coccidioidomycosis. Overall, the results suggest that Coccidioides species are not soil saprophytes, but that they have evolved to remain associated with their dead animal hosts in soil, and that Coccidioides metabolism genes, membrane-related proteins, and putatively antigenic compounds have evolved in response to interaction with an animal host.