The research advance of the medical fungal genomics

Abstract

Abstract: A serial of medical fungus genome data have been published in recent years, by which human can make a better understanding of the pathogenesis of these pathogens. Here we try to review the history of the medical fungal genomics,genome sequencing technology and introduce the development and progress of clinical important medical fungi genome.

Key words: fungi, whole genome sequencing, Candida, Cryptococcus, Aspergillus, Penicillium, Dermatophytes, Zygomycetes

CLC Number:

R379

ZHAN Ping, WANG Chong, LIU Wei-da. The research advance of the medical fungal genomics[J]. Chinese Journal of Mycology, 2013, 8(4): 234-240.

References

[1] Jones T, Federspiel NA, Chibana H,et al. The diploid genome sequence of Candida albicans[J].Proc Natl Acad Sci USA,2004, 101(19):7329-7334.
[2] Odds FC, Brown AJ, Gow NA. Candida albicans genome sequence: a platform for genomics in the absence of genetics[J]. Genome Biol,2004,5(7):230.
[3] 李筱芳,刘维达. 医学真菌基因组学的研究进展[J]. 微生物与感染,2006,1(1):53-56.
[4] Butler G, Rasmussen MD, Lin MF,et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes[J]. Nature.2009, 4,459(7247):657-662.
[5] Inglis DO, Arnaud MB, Binkley J,et al. The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata [J].Nucleic Acids Res,2012,40(Database issue):D667-674.
[6] Sabiiti W, May RC. Mechanisms of infection by the human fungal pathogen Cryptococcus neoformans [J].Future Microbiol,2012,7(11):1297-1313.
[7] Loftus BJ, Fung E, RoncagliaP,et al. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans [J]. Science, 2005,25,307(5713):1321-1324.
[8] Lengeler KB, Fox DS, Fraser JA,et al. Mating-type locus of Cryptococcus neoformans : a step in the evolution of sex chromosomes[J]. Eukaryot Cell, 2002,1(5):704-718.
[9] D'Souza CA, Kronstad JW, Taylor G,et al. Genome variation in Cryptococcus gattii,an emerging pathogen of immunocompetenthosts[J]. MBio,2011,8,2(1):e00342-10.
[10] Nierman WC, Pain A, Anderson MJ,et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus [J]. Nature,2005,22;438(7071):1151-1156.
[11] Bok JW, Balajee SA, Marr KA, et al. A regulator of morphogenetic fungal virulence factors[J].Eukaryot Cell,2005,4(9):1574-1582.
[12] Ronning CM, Fedorova ND, Bowyer P,et al. Genomics of Aspergillus fumigatus [J]. Rev Iberoam Micol,2005,22(4):223-228.
[13] Nierman WC, Pain A, Anderson MJ, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus [J]. Nature,2005,438(7071):1151-1156.
[14] Fedorova ND, Khaldi N, JoardarVS,etal.Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus [J]. PLoS Genet,2008,4(4):e1000046.
[15] JoardarV, Abrams NF, Hostetler J, et al.Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability[J]. BMC Genomics, 2012,13(1):698.
[16] Graser Y, Scott J, Summerbell R. The new species concept in dermatophytes-a polyphasic approach[J]. Mycopathologia,2008,166(5-6): 239-256.
[17] Achterman RR, White TC. A foot in the door for dermatophyte research[J]. PLoS Pathog,2012,8(3):e1002564.
[18] Burmester A, Shelest E, Glockner G, et al. Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi[J]. Genome Biol,2011,12(1):R7.
[19] The Broad Institute (2011) Dermatophyte Comparative Database. Available: http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiHome.html. Accessed 2 March 2012.
[20] Heddergott C, Bruns S, Nietzsche S, et al. The Arthroderma benhamiae hydrophobin HypA mediates hydrophobicity and influences recognition by human immune effector cells[J]. Eukaryot Cell,2012,11(5):673-82.
[21] Martinez DA, Oliver BG, Graser Y, et al. Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals Candidate genes involved in infection[J]. MBio,2012,3(5):e00259-12.
[22] Machida M, Asai K, Sano M,et al. Genome sequencing and analysis of Aspergillusoryzae[J]. Nature,2005,438(7071):1157-1161.
[23] Woo PC, Lau SK, Liu B,et al. Draft genome sequence of Penicillium marneffei strain PM1[J]. Eukaryot Cell,2011,10(12):1740-1741.
[24] Xu J, Saunders CW, Hu P,et al. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens[J]. Proc Natl Acad Sci USA,2007, 104(47):18730-1835.
[25] Ma LJ, van der Does HC, Borkovich KA,et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium[J]. Nature,2010,464(7287):367-373.
[26] Sharpton TJ, Stajich JE, Rounsley SD, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives[J]. Genome Res,2009,19(10):1722-1731.
[27] Desjardins CA, Champion MD, Holder JW,et al. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis[J]. PLoS Genet, 2011,7(10):e1002345.
[28] Köser CU, Ellington MJ, Cartwright EJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology[J]. PLoS Pathog, 2012,8(8):e1002824.