Chapter 9 : The Genomes: Tools for Comparative Genomics and Expression Analysis

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

The Genomes: Tools for Comparative Genomics and Expression Analysis, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816858/9781555815011_Chap09-1.gif /docserver/preview/fulltext/10.1128/9781555816858/9781555815011_Chap09-2.gif


This chapter describes the genomic resources available for and and discusses selected examples of the application of the resources to address questions relevant to virulence. It appears that in , natural selection is gradually lengthening short introns and shortening longer introns toward a modal size, which presumably provides an increased level of evolutionary fitness. The current picture, however, may be refined in light of future sequencing of related genomes. Although several studies employed subtractive hybridization methods and differential display to identify genes with specific patterns of regulation, the chapter focuses on experiments with microarrays and serial analysis of gene expression (SAGE) methods. The influence of temperature on gene expression with a shotgun genomic DNA microarray containing 6,274 elements is described in the chapter. The shotgun microarray was used in additional transcriptome profiling experiments to identify targets of Mga2, and these included genes for fatty acid biosynthesis. This study serves to focus attention on fatty acid and sterol metabolism as important aspects of the response to temperature and other stresses. The genome sequences have enabled a series of transcriptome analyses with oligonucleotide microarrays and serial analysis of gene expression. The studies on genome sequences are becoming standard in the analysis of complex traits and the impact of mutations and drug treatments. There is a clear need for a central, curated database for the cryptococcal genome sequences and related resources such as mutant phenotypes, transcriptome and proteome data, protein interaction data, literature, and community information.

Citation: Kronstad J, Loftus B, Lodge J. 2011. The Genomes: Tools for Comparative Genomics and Expression Analysis, p 115-126. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch9

Key Concept Ranking

Gene Expression and Regulation
Fatty Acid Biosynthesis
Cell Wall Proteins
Multilocus Sequence Typing
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Hybridization of the genomes of the progenitor strains NIH12 ( α) and NIH433 ( ) to the tiling array of the reference strain JEC21. Regions with higher variability in log2 ratios in the NIH12 and NIH433 genomes are more divergent from the JEC21 sequence; regions with log2 ratios close to zero have greater similarity. A reciprocal pattern of similar and divergent segments is found upon hybridization of genomes of NIH12 and NIH433 to the JEC21 array. The scale of chromosome coordinates for the JEC21 genome is indicated at the top of the figure, and gaps in the chromosomes represent putative centromeric regions ( ). The borders of segments are likely sites of recombination events that occurred during the cross between strains NIH12 and NIH433 and the subsequent backcrossing to obtain JEC21 ( ). Reproduced from Hu et al. ( ).

Citation: Kronstad J, Loftus B, Lodge J. 2011. The Genomes: Tools for Comparative Genomics and Expression Analysis, p 115-126. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch9
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Alspaugh, J. A.,, J.R. Perfect, and, J. Heitman. 1997. Cryptococcus neoformans mating and virulence are regulated by the G-protein alpha subunit GPA1 and cAMP. Genes Dev. 11:32063217.
2. Bahn, Y. S.,, S. Geunes-Boyer, and, J. Heitman. 2007. Ssk2 mitogen-activated protein kinase kinase kinase governs divergent patterns of the stress-activated Hog1 signaling pathway in Cryptococcus neoformans. Eukaryot. Cell 6:22782289.
3. Baker, L. G.,, C.A. Specht,, M.J. Donlin,, and J. K. Lodge. 2007. Chitosan, the deacetylated form of chitin, is necessary for cell wall integrity in Cryptococcus neoformans. Eukaryot. Cell 6:855867.
4. Barluzzi, R.,, S. Saleppico,, A. Nocentini, J. R. Boelaert,, R. Neglia, F. Bistoni,, and E. Blasi. 2002. Iron overload exacerbates experimental meningoencephalitis by Cryptococcus neoformans. J. Neuroimmunol. 132:140146.
5. Bartlett, K. H., S. E. Kidd, and, J. W. Kronstad. 2007. The emergence of Cryptococcus gattii in British Columbia and the Pacific Northwest. Curr. Fungal Infect. Rep. 1:108115.
6. Biondo, C.,, C. Beninati,, D. Delfino, M. Oggioni,, G. Mancuso,, A. Midiri,, M. Bombaci,, and G. Teti. 2002. Identification and cloning of a cryptococcal deacetylase that produces protective immune responses. Infect. Immun. 70:23832391.
7. Biondo, C.,, G. Mancuso,, A. Midiri, M. Bombaci,, L. Messina, C. Beninati,, and G. Teti. 2006. Identification of major proteins secreted by Cryptococcus neoformans. FEMS Yeast Res. 6:645651.
8. Chaffin, W. L. 2008. Candida albicans cell wall proteins. Microbiol. Mol. Biol. Rev. 72:495544.
9. Chang, Y. C.,, C.M. Bien,, H. Lee, P. J. Espenshade,, and K. J. Kwon-Chung. 2007. Sre1p, a regulator of oxygen sensing and sterol homeostasis, is required for virulence in Cryptococcus neoformans. Mol. Microbiol. 64:614629.
10. Chow, E. D.,, O.W. Lui,, S. O’Brien,, and H. D. Madhani. 2007. Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature. Curr. Genet. 52:137148.
11. Chun, C. D., O. W. Liu, and, H. D. Madhani. 2007. A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathog. 3:e22.
12. Cramer, K. L.,, Q.D. Gerrald,, C. B. Nichols, M. S. Price,, and J. A. Alspaugh. 2006. Transcription factor Nrg1 mediates capsule formation, stress response, and pathogenesis in Cryptococcus neoformans. Eukaryot. Cell 5:11471156.
13. Denikus, N.,, F. Orfaniotou,, G. Wulf, P. F. Lehmann,, M. Monod,, and U. Reichard. 2005. Fungal antigens expressed during invasive aspergillosis. Infect. Immun. 73:47044713.
14. D’Souza, C. A.,, J.A. Alspaugh,, C. Yue,, T. Harashima,, G. M Cox,, J. R. Perfect,, and J. Heitman. 2001. Cyclic AMP-dependent protein kinase controls virulence of the fungal pathogen Cryptococcus neoformans. Mol. Cell Biol. 21:31793191.
15. Eigenheer, R. A.,, Y. Jin Lee, E. Blumwald,, B.S. Phinney,, and A. Gelli. 2007. Extracellular glycosylphosphatidylinositol-anchored mannoproteins and proteases of Cryptococcus neoformans. FEMS Yeast Res. 7:499510.
16. Fan, W.,, P. R. Kraus,, M.J. Boily,, and J. Heitman. 2005. Cryptococcus neoformans gene expression during murine macrophage infection. Eukaryot. Cell 4:14201433.
17. Forche, A.,, J. Xu,, R. Vilgalys, and, T. G. Mitchell. 2000. Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms and other markers. Fungal Genet. Biol. 31:189203.
18. Fraser, J. A.,, J.C. Huang,, R. Pukkila-Worley,, J. A Alspaugh,, T. G. Mitchell,, and J. Heitman. 2005. Chromosomal translocation and segmental duplication in Cryptococcus neoformans. Eukaryot. Cell 4:401406.
19. Fries, B. C.,, F. Chen,, B.P. Currie,, and A. Casadevall. 1996. Karyotype instability in Cryptococcus neoformans infection. J. Clin. Microbiol. 34:15311534.
20. Gygi, S. P.,, Y. Rochon,, B.R. Franza,, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19:172030.
21. Heitman, J.,, A. Casadevall,, J. K. Lodge, and, J. R. Perfect. 1999. The Cryptococcus neoformans genome sequencing project. Mycopathologia 148:17.
22. Heitman, J.,, B. Allen,, J. A. Alspaugh, and, K. J. Kwon-Chung. 1999. On the origins of congenic MATalpha and MATa strains of the pathogenic yeast Cryptococcus neoformans. Fungal Genet. Biol. 28:15.
23. Hu, G.,, I. Liu,, A. Sham, J. E. Stajich,, F.S. Dietrich,, and J. W. Kronstad. 2008. Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biol. 9:R41.
24. Hu, G.,, B.R. Steen,, T. Lian, A. P. Sham,, N. Tam, K. L. Tangen,, and J. W. Kronstad. 2007. Transcriptional regulation by protein kinase A in Cryptococcus neoformans. PLoS Path. 3:e42.
25. Huang, C.,, S.H. Nong,, M.K. Mansour,, C.A. Specht,, and S. M. Levitz. 2002. Purification and characterization of a second immunoreactive mannoprotein from Cryptococcus neoformans that stimulates T-cell responses. Infect. Immun. 70:54855493.
26. Hughes, S. S., C. O. Buckley, and, D. E. Neafsey. 2008. Complex selection on intron size in Cryptococcus neoformans. Mol. Biol. Evol. 25:247253.
27. Jacobson, E. S., A. P. Goodner, and, K. J. Nyhus. 1998. Ferrous iron uptake in Cryptococcus neoformans. Infect. Immun. 66:41694175.
28. Jung, W. H.,, A.P. Sham,, T.S. Lian,, A. Singh,, D. Kosman,, and J. W. Kronstad. 2008. Iron source preference and regulation of iron uptake in the AIDS-associated pathogen Cryptococcus neoformans. PLoS Pathog. 4:e45.
29. Jung, W. H.,, A. Sham,, R. White, and, J. W. Kronstad. 2006. Iron regulation of the major virulence factors in the AIDS-associated pathogen Cryptococcus neoformans. PLoS Biol. 4:e410.
30. Jung, W. H., and, J. W. Kronstad. 2007. Iron and fungal pathogenesis: a case study with Cryptococcus neoformans. Cell. Microbiol. 10:277284.
31. Kavanaugh, L. A., J. A. Fraser, and, F. S. Dietrich. 2006. Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment. Mol. Biol. Evol. 23:18791890.
32. Kraus, P. R.,, M.J. Boily,, S.S. Giles,, J. E Stajich,, A. Allen,, G. M Cox,, F.S. Dietrich,, J. R. Perfect,, and J. Heitman. 2004. Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray. Eukaryot. Cell 3:12491260.
33. Lengeler, K. B.,, G.M. Cox, and, J. Heitman. 2001. Serotype AD strains of Cryptococcus neoformans are diploid or aneuploid and are heterozygous at the mating-type locus. Infect. Immun. 69:115122.
34. Levitz, S. M., and, C. A. Specht. 2006. The molecular basis for the immunogenicity of Cryptococcus neoformans mannoproteins. FEMS Yeast Res. 6:513524.
35. Levitz, S. M.,, S. Nongn, M. K. Mansour,, C. Huang,, and C. A. Specht. 2001. Molecular characterization of a mannoprotein with homology to chitin deacetylases that stimulates T cell responses to Cryptococcus neoformans. Proc. Natl. Acad. Sci. USA 98:1042210427.
36. Lian, T.,, M.I. Simmer,, C. A. D’Souza,, B.R. Steen,, S. D Zuyderduyn,, S.J. Jones,, M. A. Marra,, and J. W. Kronstad. 2005. Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans. Mol. Microbiol. 55:14521472.
37. Lin, X.,, J. C. Huang,, T.G. Mitchell,, and J. Heitman. 2006. Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation. PLoS Genet. 2:e187.
38. Litvintseva, A. P.,, R. Thakur,, R. Vilgalys, and, T. G. Mitchell. 2006. Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana. Genetics 172:22232238.
39. Liu, O. W.,, C.D. Chun,, E.D. Chow,, C. Chen,, H. D. Madhani,, and S. M. Noble. 2008. Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell 135:174188.
40. Loftus, B. J.,, E. Fung, P. Roncaglia,, D. Rowley,, P. Amedeo,, D. Bruno,, J. Vamathevan,, M. Miranda,, I. J. Anderson,, J. A. Fraser,, J. E Allen,, I.E. Bosdet,, M. R Brent,, R. Chiu,, T. L Doering,, M.J. Donlin,, C. A. D’Souza,, D. S Fox,, V. Grinberg,, J. Fu,, M. Fukushima,, B. J Haas,, J.C. Huang,, G. Janbon,, S. J Jones,, H.L. Koo,, M. I Krzywinski,, K. J. Kwon-Chung,, K. B Lengeler,, R. Maiti,, M. A Marra,, R.E. Marra,, C. A Mathewson,, T.G. Mitchell,, M. Pertea,, F. R Riggs,, S.L. Salzberg,, J. E Schein,, A. Shvartsbeyn,, H. Shin,, M. Shumway,, C. A Specht,, B.B. Suh,, A. Tenney,, T. R Utterback,, B.L. Wickes,, J. R Wortman,, N.H. Wye,, J. W Kronstad,, J.K. Lodge,, J. Heitman,, R. W Davis,, C. M. Fraser,, and R. W. Hyman. 2005. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307:13211324.
41. Marra, R. E.,, J.C. Huang,, E. Fung,, K. Nielsen,, J. Heitman,, R. Vilgalys,, and T. G. Mitchell. 2004. A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans). Genetics 167:619631.
42. Meyer, W.,, A. Castaneda,, S. Jackson,, M. Huynh,, E. Castaneda, and the IberoAmerican Cryptococcal Study Group. 2003. Molecular typing of IberoAmerican Cryptococcus neoformans isolates. Emerg. Infect. Dis. 9:189195.
43. Missall, T. A., M. E. Pusateri, and, J. K. Lodge. 2004. Thiol peroxidase is critical for virulence and resistance to nitric oxide and peroxide in the fungal pathogen, Cryptococcus neoformans. Mol. Microbiol. 51:14471458.
44. Missall, T. A.,, M.E. Pusateri,, M.J. Donlin,, K. T Chambers,, J. A. Corbett,, and J. K. Lodge. 2006. Posttranslational, translational, and transcriptional responses to nitric oxide stress in Cryptococcus neoformans: implications for virulence. Eukaryot. Cell 5:518529.
45. Montagnoli, C.,, S. Sandini,, A. Bacci, L. Romani,, and R. La Valle. 2004. Immunogenicity and protective effect of recombinant enolase of Candida albicans in a murine model of systemic candidiasis. Med. Mycol. 42:319324.
46. Nombela, C., C. Gil, and, W. L. Chaffin. 2006. Non-conventional protein secretion in yeast. Trends Microbiol. 14:1521.
47. Nyhus, K. J., A. T. Wilborn, and, E. S. Jacobson. 1997. Ferric iron reduction by Cryptococcus neoformans. Infect. Immun. 65:434438.
48. Nyhus, K. J., and, E. S. Jacobson. 1999. Genetic and physiologic characterization of ferric/cupric reductase constitutive mutants of Cryptococcus neoformans. Infect. Immun. 5:23572365.
49. Panepinto, J.,, K. Komperda,, S. Frases, Y. D. Park,, J. T. Djordjevic, A. Casadevall,, and P. R. Williamson. 2009. Sec6-dependent sorting of fungal extracellular exosomes and laccase of Cryptococcus neoformans. Mol. Microbiol. 71:11651176.
50. Pukkila-Worley, R.,, Q.D. Gerrald,, P.R. Kraus,, M.J. Boily,, M. J Davis,, S.S. Giles,, G. M Cox,, J. Heitman,, and J. A. Alspaugh. 2005. Transcriptional network of multiple capsule and melanin genes governed by the Cryptococcus neoformans cyclic AMP cascade. Eukaryot. Cell 4:190201.
51. Rodrigues, M. L.,, E.S. Nakayasu,, D.L. Oliveira,, L. Nimrichter,, J. D Nosanchuk,, I. C. Almeida,, and A. Casadevall. 2008. Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence. Eukaryot. Cell 7:5867.
52. Rodrigues, M. L.,, L. Nimrichter,, D. L. Oliverira,, S. Frases,, K. Miranda,, O. Zaragoza,, M. Alvarez,, A. Nakouzi,, M. Feldmesser,, and A. Casadevall. 2007. Vesicular polysaccharide export in Cryptococcus neoformans is a eukaryotic solution to the problem of fungal trans-cell wall transport. Eukaryot. Cell 6:4859.
53. Roy, S. W., D. Penny, and, D. E. Neafsey. 2007. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol. Biol. Evol. 24:11401148.
54. Schein, J.,, K. Tangen,, R. Chiu,, H. Shin,, K. Lengeler,, K. MacDonald,, I. Bosdet,, J. Heitman,, S. J. M. Jones,, M. Marra,, and J. Kronstad. 2002. Physical maps for sequence analysis of the genomes of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 12:14451453.
55. Sharpton, T. J.,, D.E. Neafsey,, J.E. Galagan,, and J. W. Taylor. 2008. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 9:R24.
56. Steen, B. R.,, T. Lian, S. Zuyderduyn,, W.K. MacDonald,, M. Marra,, S. J. Jones,, and J. W. Kronstad. 2002. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 12:13861400.
57. Steen, B. R.,, S. Zuyderduyn,, D. L. Toffaletti,, M. Marra,, S. J. Jones,, J. R. Perfect,, and J. Kronstad. 2003. Cryptococcus neoformans gene expression during experimental cryptococcal meningitis. Eukaryot. Cell 2:13361349.
58. Sun, S., and, J. Xu. 2007. Genetic analyses of a hybrid cross between serotypes A and D strains of the human pathogenic fungus Cryptococcus neoformans. Genetics 177:14751486.
59. Sun, S., and, J. Xu. 2009. Chromosomal rearrangements between serotype A and D strains in Cryptococcus neoformans. PLoS ONE 4:e5524.
60. Tangen, K. T.,, W.H. Jung,, A. Sham, T. S. Lian,, and J. W. Kronstad. 2007. The iron and cAMP regulated gene SIT1 influences siderophore utilization, melanization and cell wall structure in Cryptococcus neoformans. Microbiology 153:2941.
61. Tarentino, A. L., C. M. Gómez, and, T. H. Plummer, Jr. 1985. Deglycosylation of asparagine-linked glycans by peptide:N-glycosidase F. Biochemistry 24:46654671.
62. Tenney, A. E.,, R.H. Brown,, C. Vaske,, J. K Lodge,, T. L. Doering,, and M. R. Brent. 2004. Gene prediction and verification in a compact genome with numerous small introns. Genome Res. 14:23302335.
63. Vartivarian, S. E.,, E.J. Anaissie,, R.E. Cowart,, H. A Sprigg,, M. J. Tingler,, and E. S. Jacobson. 1993. Regulation of cryptococcal capsular polysaccharide by iron. J. Infect. Dis. 167:186190.
64. Velculescu, V. E.,, L. Zhang,, B. Vogelstein, and, K. W. Kinzler. 1995. Serial analysis of gene expression. Science 270:484487.
65. Wang, Z., M. Gerstein, and, M. Snyder. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:5763.
66. Xu, J.,, R.Y. Ali,, D.A. Gregory,, D. Amick,, S. E Lambert,, H.J. Yoell,, R. J. Vilgalys,, and T. G. Mitchell. 2000. Uniparental mitochondrial transmission in sexual crosses in Cryptococcus neoformans. Curr. Microbiol. 40:269273.
67. Xu, J., R. Vilgalys, and, T. G. Mitchell. 2000. Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. Mol. Ecol. 9:14711481.
68. Young, E. T.,, K. M. Dombek,, C. Tachibana,, and T. Ideker. 2003. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J. Biol. Chem. 278:2614626158.
69. Young, M.,, S. Macias,, D. Thomas, and, F. L. Wormley, Jr. 2009. A proteomic-based approach for the identification of immunodominant Cryptococcus neoformans proteins. Proteomics 9:25782588.


Generic image for table

and strains with sequenced genomes

Citation: Kronstad J, Loftus B, Lodge J. 2011. The Genomes: Tools for Comparative Genomics and Expression Analysis, p 115-126. In Heitman J, Kozel T, Kwon-Chung K, Perfect J, Casadevall A (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555816858.ch9

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error