Genomic and population analyses of the mating type loci in Coccidioides species reveal evidence for sexual reproduction and gene acquisition

Eukaryotic Cell

Volumn 6, Issue 7, 2007, Pages 1189-1199

  Mandel, M Alejandra ^a,b   Barker, Bridget M ^a,b   Kroken, Scott ^a,b   Rounsley, Steven D ^a   Orbach, Marc J ^a,b  

^a UNIVERSITY OF ARIZONA   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; FUNGAL PROTEIN; MEMBRANE PROTEIN; NUCLEAR PROTEIN;

ARTICLE; CLASSIFICATION; COCCIDIOIDES; FUNGAL GENE; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM; PHYLOGENY; PHYSIOLOGY; REPRODUCTION;

COCCIDIOIDES; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; FUNGAL PROTEINS; GENES, MATING TYPE, FUNGAL; GENOME, FUNGAL; MEMBRANE PROTEINS; NUCLEAR PROTEINS; PHYLOGENY; REPRODUCTION; TRANSCRIPTION, GENETIC;

ASCOMYCOTA; COCCIDIOIDES; COCCIDIOIDES IMMITIS; COCCIDIOIDES POSADASII; FUNGI; UNCINOCARPUS REESII;

EID: 34447565176     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.00117-07     Document Type: Article

References (37)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic Local Alignment Search Tool. J. Mol. Biol. 215:403-410.
2. Beauvoit, B., O. Bunoust, B. Guerin, and M. Rigoulet. 1999. ATP-regulation of cytochrome oxidase in yeast mitochondria: role of subunit Via. Eur. J. Biochem. 263:118-127.
3. Berriman, M., and K. Rutherford. 2003. Viewing and annotating sequence data with Artemis. Brief. Bioinformatics 4:124-132.
4. Bubnick, M., and A. G. Smulian. 2007. The MAT1 locus of Histoplasma capsulatum is responsive in a mating type-specific manner. Eukaryot. Cell 6:616-621.
5. Burt, A., D. A. Carter, G. L. Koenig, T. J. White, and J. W. Taylor. 1996. Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. Proc. Natl. Acad. Sci. USA 93:770-773.
6. Burt, A., B. M. Dechairo, G. L. Koenig, D. A. Carter, T. J. White, and J. W. Taylor. 1997. Molecular markers reveal differentiation among isolates of Coccidioides immitis from California, Arizona and Texas. Mol. Ecol. 6:781-786.
7. Coppin, E., R. Debuchy, S. Arnaise, and M. Picard. 1997. Mating types and sexual development in filamentous ascomycetes. Microbiol. Mol. Biol. Rev. 61:411-428.
8. Debuchy, R., and B. G. Turgeon. 2006. Mating-type structure, evolution, and function in Euascomycetes, p. 293-323. In U. Kües and R. Fischer (ed.), The Mycota, vol. I. Growth, differentiation, and sexuality, 2nd ed. Springer, Berlin, Germany.
9. Delcher, A. L., A. Phillippy, J. Carlton, and S. L. Salzberg. 2002. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30:2478-2483.
10. Dyer, P. S., M. Paoletti, and D. B. Archer. 2003. Genomics reveals sexual secrets of Aspergillus. Microbiology 149:2301-2303.
11. Fisher, M. C., G. L. Koenig, T. J. White, G. San-Blas, R. Negroni, I. G. Alvarez, B. Wanke, and J. W. Taylor. 2001. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc. Natl. Acad. Sci. USA 98:4558-4562.
12. Fisher, M. C., T. J. White, and J. W. Taylor. 1999. Primers for genotyping single nucleotide polymorphisms and microsatellites in the pathogenic fungus Coccidioides immitis. Mol. Ecol. 8:1082-1084.
13. 12a.Fisher, M. C., G. L. Koenig, T. J. White, and J. T. Taylor. 2002. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia 94:73-84.
14. Fraser, J. A., J. E. Stajich, E. J. Tarcha, G. T. Cole, D. O. Inglis, A. Sil, and J. Heitman. 2007. Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. Eukaryot. Cell 6:622-629.
15. Galagan, J. E., S. E. Calvo, C. Cuomo, L. J. Ma, J. R. Wortman, S. Batzoglou, S. I. Lee, M. Basturkmen, C. C. Spevak, J. Clutterbuck, V. Kapitonov, J. Jurka, C. Scazzocchio, M. Farman, J. Butler, S. Purcell, S. Harris, G. H. Braus, O. Draht, S. Busch, C. D'Enfert, C. Bouchier, G. H. Goldman, D. Bell-Pedersen, S. Griffiths-Jones, J. H. Doonan, J. Yu, K. Vienken, A. Pain, M. Freitag, E. U. Selker, D. B. Archer, M. A. Penalva, B. R. Oakley, M. Momany, T. Tanaka, T. Kumagai, K. Asai, M. Machida, W. C. Nierman, D. W. Denning, M. Caddick, M. Hynes, M. Paoletti, R. Fischer, B. Miller, P. Dyer, M. S. Sachs, S. A. Osmani, and B. W. Birren. 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438:1105-1115.
16. Gowda, M., C. Jantasuriyarat, R. A. Dean, and G. L. Wang. 2004. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol. 134:890-897.
17. Greene, D. R., G. Koenig, M. C. Fisher, and J. W. Taylor. 2000. Soil isolation and molecular identification of Coccidioides immitis. Mycologia 92:406-410.
18. Hillis, D. M., C. Moritz, and B. K. Mable (ed.). 1996. Molecular systematics, 2nd ed. Sinauer Associates, Inc., Sunderland, MA.
19. Johnson, R. E., C. A. Torres-Ramos, T. Izumi, S. Mitra, S. Prakash, and L. Prakash. 1998. Identification of APN2, the Saccharomyces cerevisiae homolog of the major human AP endonuclease HAP1, and its role in the repair of abasic sites. Genes Dev. 12:3137-3143.
20. Kellner, E. M., K. I. Orsborn, E. M. Siegel, M. A. Mandel, M. J. Orbach, and J. N. Galgiani. 2005. Coccidioides posadasii contains a single 1,3-beta-glucan synthase gene that appears to be essential for growth. Eukaryot. Cell 4:111-120.
21. Kirkland, T. N., and J. Fierer. 1996. Coccidioidomycosis: a reemerging infectious disease. Emerg. Infect. Dis. 2:192-199.
22. Koufopanou, V., A. Burt, and J. W. Taylor. 1997. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. USA 94:5478-5482.
23. Kronstad, J. W., and C. Staben. 1997. Mating type in filamentous fungi. Annu. Rev. Genet. 31:245-276.
24. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinformatics 5:150-163.
25. Kwon-Chung, K. J., R. J. Weeks, and H. W. Larsh. 1974. Studies on Emmonsiella capsulata (Histoplasma capsulatum). II. Distribution of the two mating types in 13 endemic states of the United States. Am. J. Epidemiol. 99:44-49.
26. Lutzoni, F., F. Kauff, C. J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T. Y. James, E. Baloch, M. Grube, V. Reeb, V. Hofstetter, C. Schoch, A. E. Arnold, J. Miadlikowska, J. Spatafora, D. Johnson, S. Hambleton, M. Crockett, R. Shoemaker, S. Hambleton, M. Crockett, R. Shoemaker, G. H. Sung, R. Lucking, T. Lumbsch, K. O'Donnell, M. Binder, P. Diederich, D. Ertz, C. Gueidan, K. Hansen, R. C. Harris, K. Hosaka, Y. W. Lim, B. Matheny, H. Nishida, D. Pfister, J. Rogers, A. Rossman, I. Schmitt, H. Sipman, J. Stone, J. Sugiyama, R. Yahr, and R. Vilgalys. 2004. Assembling the fungal tree of life: progress, classification and evolution of subcellular traits. Am. J. Bot. 91:1446-1480.
27. Mandel, M. A., J. N. Galgiani, S. Kroken, and M. J. Orbach. 2006. Coccidioides posadasii contains single chitin synthase genes corresponding to classes I to VII. Fungal Genet. Biol. 43:775-788.
28. Metzenberg, R. L., and N. L. Glass. 1990. Mating type and mating strategies in Neurospora. Bioessays 12:53-59.
29. Nielsen, K., R. E. Marra, F. Hagen, T. Boekhout, T. G. Mitchell, G. M. Cox, and J. Heitman. 2005. Interaction between genetic background and the mating-type locus in Cryptococcus neoformans virulence potential. Genetics 171:975-983.
30. Omieczynski, D. T., and F. E. Swatek. 1967. The comparison of two methods for the direct isoltion of Coccidioides immitis from soil using three different media, p. 265-272. In L. Ajello (ed.), Coccidioidomycosis. University of Arizona Press, Tucson, AZ.
31. Paoletti, M., C. Rydholm, E. U. Schwier, M. J. Anderson, G. Szakacs, F. Lutzoni, J. P. Debeaupuis, J. P. Latge, D. W. Denning, and P. S. Dyer. 2005. Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus. Curr. Biol. 15:1242-1248.
32. Park, B. J., K. Sigel, V. Vaz, K. Komatsu, C. McRill, M. Phelan, T. Colman, A. C. Comrie, D. W. Warnock, J. N. Galgiani, and R. A. Hajjeh. 2005. An epidemic of coccidioidomycosis in Arizona associated with climatic changes, 1998-2001. J. Infect. Dis. 191:1981-1987.
33. Rydholm, C., P. S. Dyer, and F. Lutzoni. 2007. DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri. Eukaryot. Cell 6:868-874.
34. Saha, S., A. B. Sparks, C. Rago, V. Akmaev, C. J. Wang, B. Vogelstein, K. W. Kinzler, and V. E. Velculescu. 2002. Using the transcriptome to annotate the genome. Nat. Biotechnol. 20:508-512.
35. Turgeon, G., and O. C. Yoder. 2000. Proposed nomenclature for mating type genes of filamentous ascomycetes. Fungal Genet. Biol. 31:1-5.
36. Valdivia, L., D. Nix, M. Wright, E. Lindberg, T. Fagan, D. Lieberman, T. Stoffer, N. M. Ampel, and J. N. Galgiani. 2006. Coccidioidomycosis as a common cause of community-acquired pneumonia. Emerg. Infect. Dis. 12:958-962.
37. Woo, P. C. Y., K. T. K. Chong, H. Tse, J. J. Cai, C. C. Y. Lau, A. C. Zhou, S. K. P. Lau, and K. Y. Yuen. 2006. Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. FEBS Lett. 580:3409-3416.