Genomics for Fungi

  • J. W. Bennett
  • Jonathan Arnold
Part of the The Mycota book series (MYCOTA, volume 8)


Since 1995, the genomes of dozens of bacteria and several model eukaryotes have been completely sequenced and these data have been deposited in public databases. With the exception of the yeast Saccharomyces cerevisiae, fungal genomes were not among these early genomics accomplishments. Nevertheless, despite a slow start, fungal genomics is now poised to reveal a comprehensive picture of fungal gene structure and function, to resolve questions about evolutionary relationships among mycelial fungi, and to decipher the biochemical and cellular relationships between fungi and other eukaryotic life forms. Genomics databases and their accompanying bioinformatics tools are among the most powerful scientific resources available to contemporary fungal cell biologists.


Fission Yeast Phytophthora Infestans Cryptococcus Neoformans Neurospora Crassa Aspergillus Nidulans 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Adams MD, Kelley JM, Gocayne JD et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656PubMedCrossRefGoogle Scholar
  2. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD et al. (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195PubMedCrossRefGoogle Scholar
  3. Adams TH, Yu JH (1998) Coordinate control of secondary metabolite production and asexual sporulation in Aspergillus nidulans. Curr Opin Microbiol 1:674–677PubMedCrossRefGoogle Scholar
  4. Aign V, Schulte U, Hoheisel JD (2001) Hybridization mapping of Neurospora crassa linkage groups II and V. Genetics 157:1015–1020PubMedGoogle Scholar
  5. Alberts BM, Botsein D, Brenner S (1988) Report of the Committee on Mapping and Sequencing the Human Genome, National Academy of Sciences, Washington, DCGoogle Scholar
  6. Alec M, Gold MH (1991) Genetics and molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium, In: Bennett JW, Lasure LL (eds) More Gene Manipulations in Fungi. Academic Press, New York, pp 320–341Google Scholar
  7. Altmann-Johl R, Philippsen P (1996) AgTHR4, a new selection marker for transformation of the filamentous fungus Ashbya gossypii, maps in a four-gene cluster that is conserved between A. gossypii and Saccharomyces cerevisiae. Mol Gen Genet 250:69–80PubMedGoogle Scholar
  8. Altschul FS, Gish W, Millcr W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  9. Amar YG, Moore MM (1998) Mapping of the nitrate-assimilation gene cluster (crnA-niiA-niaD) and characterization of the nitrite reductase gene (niiA) in the opportunistic fungal pathogen Aspergillus fumigatus. Curr Genet 33:206–215CrossRefGoogle Scholar
  10. Amber D (2000) Production genomics. The Scientist 14:1, 14, 16, 19Google Scholar
  11. Anonymous (2000) Abstracts Third International Symposium on Fungal Genomics, International Business Communications, Southborough, MassachusettsGoogle Scholar
  12. Aramayo R, Bennett JW (1997) The importance of fungal genomes. Am Soc Microbiol News 63:176–177Google Scholar
  13. Aravind L, Watanabe H, Lipman DJ, Koonin EV (2000) Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci USA 97:11319–11324PubMedCrossRefGoogle Scholar
  14. Arnold J (1997) Editorial. Fungal Genet Biol 21:254–257CrossRefGoogle Scholar
  15. Attwood TK, Croning MDR, Flower DR, Lewis AP, Maybe JE (2000) PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Res 28:225–227PubMedCrossRefGoogle Scholar
  16. Bailey DS, Furness LM, Dean PM (1999) New tools for quantifying molecular diversity. PharmaInformatics. Trends Suppl 6–9Google Scholar
  17. Barr DP, Aust SD (1994) Mechanisms white rot fungi use to degrade pollutants. Environ Sci Technol 28:79A-87AGoogle Scholar
  18. Beadle GW, Tatum EL (1941) Genetic control of biochemical reaction in Neurospora. Proc Natl Acad Sci USA 27:499–506PubMedCrossRefGoogle Scholar
  19. Bean LE, Dvoracheck WH, Braun EL, Errett A, Saenz GS et al. (2001) Analysis of the pdx-1 (snz-1/sno-1) region of the Neuorspora crassa genome: correlation of pyridoxine-requiring phenotypes with mutations in two structural genes. Genetics 157:1067–1075PubMedGoogle Scholar
  20. Bennett JW (1997a) Open letter to fungal researchers. Fungal Genet Biol 21:2PubMedCrossRefGoogle Scholar
  21. Bennett JW (1997b) White paper: genomics for filamentous fungi. Fungal Genet Biol 21:3–7PubMedCrossRefGoogle Scholar
  22. Bennett JW, Chang P-K, Bhatnagar D (1997) One gene to whole pathway: the role of norsolorinic acid in anatoxin research. Adv Appl Microbiol 45:1–15PubMedCrossRefGoogle Scholar
  23. Bennett JW, Lasure L (1985) Conventions for gene symbols. In: Bennett JW, Lasure L (eds) Gene manipulations in fungi. Academic Press, San Diego, pp 537–544Google Scholar
  24. Benson DA, Bogushi MS, Lipman DJ, Ostell J, Ouellette BFF (1998) GenBank. Nucleic Acids Res 26:1–7CrossRefGoogle Scholar
  25. Berbee ML, Taylor JW (1993) Dating the evolutionary radiations of the true fungi. Can J Bot 71:1114–1127CrossRefGoogle Scholar
  26. Berg P, Singer M (1992) Dealing with genes. The language of heredity. University Science Books, Mill Valley, California, p 247Google Scholar
  27. Bhandarkar SM, Machaka SA, Shete SS, Kota RN (2001) Parallel computation of a maximum likelihood estimator of a physical map. Genetics 157:1021–1043PubMedGoogle Scholar
  28. Birren B, Green ED, Klaholz S, Myers RM, Roskams J (1997) Genome Analysis, a Laboratory Manual, vol. 1.Analyzing DNA. Cold Spring Harbor Press, Cold Spring HarborGoogle Scholar
  29. Bishop M (ed) (1999) Genetic databases. Academic Press, San DiegoGoogle Scholar
  30. Blanchard AP, Hood L (1996) Sequence to array: probing the genome’s secrets. Nature Biotech 14:1649CrossRefGoogle Scholar
  31. Blattner FR, Plunkett G, Block CA, Perna NT, Burland V et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1464PubMedCrossRefGoogle Scholar
  32. Boguski MS (1995) The turning point in genomic research trends. Biochem Sci 20:295–296CrossRefGoogle Scholar
  33. Botstein D, Cherry JM (1997) Molecular linguistics: extracting information from gene and protein sequences. Proc Natl Acad Sci USA 94:5506–5507PubMedCrossRefGoogle Scholar
  34. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedGoogle Scholar
  35. Botstein D, Chervitz SA, Cherry JM (1997) Yeast as a model organism. Science 277:1259–1260PubMedCrossRefGoogle Scholar
  36. Braun EL, Halpern AL, Nelson MA, Natvig DO (2000) Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res 10:416–430PubMedCrossRefGoogle Scholar
  37. Brenner SE (1999) Errors in genome annotation. Trends Genet 15:132–133PubMedCrossRefGoogle Scholar
  38. Brocklehurst SM, Hardman CH, Johnston SJT (1999) Creating integrated computer systems for target discovery and drug discovery. PharmaInformatics. Trends Suppl 1999:12–15Google Scholar
  39. Broda PP, Birch RJ, Brooke PR, Sims PRFG (1996) Lig-nocellulose degradation by Phanerochaete chrysosporium: gene families and gene expression for a complex process. Mol Microbiol 19:923–932PubMedCrossRefGoogle Scholar
  40. Brown APJ, Gow NAR (1999) Regulatory networks controlling Candida albicans morphogenesis. Trends Microbiol 7:333–338PubMedCrossRefGoogle Scholar
  41. Brown DW, Yu J-H, Kelkar HS, Fernandes M, Nesbitt TC et al. (1996) Twenty five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc Natl Acad Sci USA 93:1418–1422PubMedCrossRefGoogle Scholar
  42. Burke DT, Carle GF, Olson MV (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:806–812PubMedCrossRefGoogle Scholar
  43. Burset M, Guigo R (1996) Evaluation of gene structure prediction programs. Genomics 34:353–367PubMedCrossRefGoogle Scholar
  44. Celegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018CrossRefGoogle Scholar
  45. Carlson M (2000) The awesome power of yeast biochemical genomics. Trends Genet 16:49–51PubMedCrossRefGoogle Scholar
  46. Casadevall A, Perfect JR (1998) Cryptococcus neoformans. ASM Press, Washington, DCGoogle Scholar
  47. Clutterbuck AJ (1973) Gene symbols in Aspergillus nidulans. Genet Res 21:291–296PubMedCrossRefGoogle Scholar
  48. Clutterbuck AJ (1994) Linkage map and locus list. In: Martinelli SD, Kinghorm JR (eds) Aspergillus fifty years on. Elsevier, Amsterdam, pp 791–805Google Scholar
  49. Clutterbuck (1997) The validity of the Aspergillus nidulans linkage map. Fungal Genet Biol 21:267–277PubMedCrossRefGoogle Scholar
  50. Cohen J (1997) The genomics gamble. Science 275:767–775PubMedCrossRefGoogle Scholar
  51. Collins FS, Gallas D (1993) A new five-year plan for the US Human Genome Project. Science 262:43–44PubMedCrossRefGoogle Scholar
  52. Collins FS, Patrinos A, Jordan E, Chakrevartie A, Gesteland R, Walters L and The members of the DOE and NIH planning groups (1998) New goals for the US Human Genome Project: 1998–2003. Science 282: 682–689PubMedCrossRefGoogle Scholar
  53. Cushion MT, Arnold JA (1998) Proposal for a Pneumocystis genome project. J Eukaryot Microbiol 44:7sCrossRefGoogle Scholar
  54. Cushion MT, Kaselis M, Stringer SL, Stringer JR (1993) Genetic stability and diversity of Pneumocystis carinii infecting rat colonies. Infect Immun 61:4801–4813PubMedGoogle Scholar
  55. Cuticchia AJ, Arnold J, Timberlake WE (1992) The use of simulated annealing in chromosome reconstruction experiments based on binary scoring. Genetics 132:591–601PubMedGoogle Scholar
  56. Davis R (2000) Neurospora: contributions of a model organism. Oxford Univ. Press, OxfordGoogle Scholar
  57. DeBacker MD, Magee PH, Pla J (2000) Recent developments in molecular genetics of Candida albicans. Annu Rev Microbiol 54:463–498CrossRefGoogle Scholar
  58. Debets F, Swart K, Hockstra RF, Bos CJ (1993) Genetic maps of eight linkage groups of Aspergillus niger based on mitotic mapping. Curr Genet 23:47–53PubMedCrossRefGoogle Scholar
  59. Demain A (1972) Riboflavin over synthesis. Annu Rev Microbiol 26:369–388PubMedCrossRefGoogle Scholar
  60. Demerec M, Adelberg AE, Clark AJ, Hartman PE (1966) A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:61–76PubMedGoogle Scholar
  61. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686PubMedCrossRefGoogle Scholar
  62. Diaz-Perez SV, Crouch VW, Orbach MC (1996) Construction and characterization of a Magnaporthe grisea bacterial artificial chromosome library. Fungal Genet Biol 20:280–288PubMedCrossRefGoogle Scholar
  63. Dujon B (1996) The yeast genome project: what did we learn? Trends Genet 12:263–270PubMedCrossRefGoogle Scholar
  64. Dunn-Coleman N, Prade R (1998) Toward a global filamentous fungus genome sequencing effort. Nature Biotech 16:5CrossRefGoogle Scholar
  65. Edman JC, Kovacs JA, Masur H, Sanit DV, Elwood HJ, Sogin ML (1988) Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature 334:519–522PubMedCrossRefGoogle Scholar
  66. Enright AJ, Illopoulos I, Kyrpides NC, Ouzounis CA (2000) Protein interaction maps for comparing genomes based on gene fusion events. Nature 402:86–90Google Scholar
  67. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194PubMedGoogle Scholar
  68. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  69. Farman ML, Leong SA (1998) Chromosome walking to the AVR1-C039 avirulence gene of Magnaporthe grisea: discrepancy between the physical and genetic maps. Genetics 150:1049–1058PubMedGoogle Scholar
  70. Fickett JW (1996) Finding genes by computer. The state of the art. Trends Genet 12:316–320PubMedCrossRefGoogle Scholar
  71. Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19:99–113PubMedCrossRefGoogle Scholar
  72. Fleischmann RD, Adams MD, White O et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae RD. Science 269:496–512PubMedCrossRefGoogle Scholar
  73. Forsburg SL, Nurse P (1991) Cell cycle regulation in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Annu Rev Cell Biol 7:227–256PubMedCrossRefGoogle Scholar
  74. Forster H, Coffey MD, Elwood H, Sogin ML (1990) Sequence analysis of the small subunit ribosomal RNAs of three zoosporic fungi and implications for fungal evolution. Mycologia 82:306–312CrossRefGoogle Scholar
  75. Fraser CM, Gacayne JD, White O et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397–403PubMedCrossRefGoogle Scholar
  76. Garber ED (1972) Cytogenetics, an introduction. McGraw Hill Book, New YorkGoogle Scholar
  77. Gaskell G, Bauer MW, Durant J, Allum NC (1999) Worlds apart? The reception of genetically modified foods in Europe and the US. Science 285:384–387PubMedCrossRefGoogle Scholar
  78. Geiser DM, Pitt JI, Taylor JW (1998) Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc Natl Acad Sci USA 95:388–393PubMedCrossRefGoogle Scholar
  79. Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genet 25:25–29CrossRefGoogle Scholar
  80. Gilbert W (1991) Toward a paradigm shift in biology. Nature 349:99PubMedCrossRefGoogle Scholar
  81. Godfrey T, West S (eds) (1996) Industrial enzymology, 2nd edn. Stockton Press, New YorkGoogle Scholar
  82. Goffeau A, Barrell BG, Bussey H, Davis RW et al. (1996) Life with 6000 genes. Science 274:546–567PubMedCrossRefGoogle Scholar
  83. Goffeau A et al. (1997) The yeast genome directory. Nature 387(Suppl):1–105Google Scholar
  84. Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR (2000) Identification of the copper regulon of Saccharomyces cerevisiae by DNA microarrays. J Biol Chem 275:32310–32316PubMedCrossRefGoogle Scholar
  85. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 97:9390–9395PubMedCrossRefGoogle Scholar
  86. Hall D, Bhandarkar SM, Wang J (2001) ODS2: a multi-platform software application for creating integrated physical and genetic maps. Genetics 157:1045–1056PubMedGoogle Scholar
  87. Hamer JE, Farrall L, Orbach MJ, Valent B, Chumley FG (1989) Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal plant pathogen. Proc Natl Acad Sci USA 86:9981–9985PubMedCrossRefGoogle Scholar
  88. Hamer L (1997) Meeting review. From genes to genomes: sequencing of filamentous fungal genomes. Fungal Genet Biol 21:8–10PubMedCrossRefGoogle Scholar
  89. Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance and conservation. Mycol Res 95:641–655CrossRefGoogle Scholar
  90. Hayles J, Nurse P (1992) Genetics of the fission yeast Schizosaccharomycespombe. Annu Rev Genet 26:373–402PubMedCrossRefGoogle Scholar
  91. Hegyi H, Gerstein M (1999) The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 288:147–164PubMedCrossRefGoogle Scholar
  92. Heitman J, Casadevall A, Leodge JK, Perfect JR (2000) The Cryptococcus neoformans genome sequencing project. Mycopath 148:1–7CrossRefGoogle Scholar
  93. Hieter P, Boguski M (1997) Functional genomics: it’s all how you read it. Science 278:601–602PubMedCrossRefGoogle Scholar
  94. Hodgson J (1994) Genome mapping the “easy” way. Bio/Technology 12: 581–584PubMedCrossRefGoogle Scholar
  95. Hoheisel JD, Maier C, Mott R, McCarthy L, Grigoriev AV (1993) High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell 73:109–120PubMedCrossRefGoogle Scholar
  96. Hughes TR, Marion MJ, Jones AR, Roberts CJ, Stoughton R et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102:109–126PubMedCrossRefGoogle Scholar
  97. Hull CM, Raisner RM, Johnson D (2000) Evidence for mating of the “asexual” yeast Candida albicans in a mammalian host. Science 289:307–310PubMedCrossRefGoogle Scholar
  98. Hyman RW (2001) Sequence data: posted vs. published. Science 291:827 International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–918CrossRefGoogle Scholar
  99. Judelson HS (1996) Recent advances in the genetics of oomycete plant pathogens. Mol Plant-Microbe Interact 9:443–449CrossRefGoogle Scholar
  100. Kafer E (1977) Meiotic and mitotic recombination in Aspergillus and its chromosomal aberrations. Adv Genet 19:33–131PubMedCrossRefGoogle Scholar
  101. Kamoun S, Hraber P, Sobral B, Nuss D, Govers F (1999) Initial assessment of gene diversity for the oomycete plant pathogen Phytophthora infestans based on expressed sequences. Fungal Genet Biol 28: 94–106PubMedCrossRefGoogle Scholar
  102. Kelkar HS, Griffith J, Case ME, Covert SF, Hall RD, Arnold J (2001) The Neurospora crassa genome: cosmid libraries sorted by chromosomes. Genetics 157:979–990PubMedGoogle Scholar
  103. Kennedy D (2001) Accepted community standards. Science 291:789PubMedCrossRefGoogle Scholar
  104. Kirk TK, Farrell RL (1987) Enzymatic “combustion,” the microbial degradation of lignin. Annu Rev Microbiol 41:465–505PubMedCrossRefGoogle Scholar
  105. Klich MA, Yu J, Mullaney EJ (1987) DNA restriction enzyme fragment polymorphism as a tool for rapid differentiation of Aspergillus flavus from Aspergillus oryzae. Exp Mycol 11:170–175CrossRefGoogle Scholar
  106. Klich MA, Montalbano B, Ehrlich K (1997) Northern analysis of aflatoxin biosynthesis genes in Aspergillus parasiticus and Aspergillus sojae. Appl Microbiol Biotech 47:246–249CrossRefGoogle Scholar
  107. Koonin EV, Mushegian AR, Rudd KE (1996) Sequencing and analysis of bacterial genomes. Curr Biol 6:404–416PubMedCrossRefGoogle Scholar
  108. Kraemer E, Wang J, Guo J, Arnold J (2001) An analysis of gene-finding approaches for neurospora crassa. Bio information (in press)Google Scholar
  109. Kron J, Gow NAR (1995) Budding yeast morphogenesis. Signalling, cytoskeleton and cell cycle. Curr Opin Cell Biol 7:845–855PubMedCrossRefGoogle Scholar
  110. Kwon-Chung KJ, Bennett JE (1992) Medical mycology. Lea & Febiger, PhiladelphiaGoogle Scholar
  111. Kupfer DM, Reece CA, Clifton SW, Roe BA, Prade RA (1997) Multicellular ascomycetous fungal genomes contain more than 8000 genes. Fungal Genet Biol 21:364–372PubMedCrossRefGoogle Scholar
  112. Kusumoto K-I, Nogata Y, Ohta H (2000) Directed deletions in the aflatoxin biosynthesis gene homolog cluster of Aspergillus oryzae. Curr Genet 37:104–111PubMedCrossRefGoogle Scholar
  113. Latge JP (1999) Aspergillus fumigatus and aspergillosis. Clin Microbiol Rev 12:310–350PubMedGoogle Scholar
  114. Lennon GG, Lehrach H (1992) Gene database for the fission yeast Schizosaccharomyces pombe. Curr Genet 21:1–11PubMedCrossRefGoogle Scholar
  115. Leung H, Borromeo ES, Bernardo MA, Notteghem JL (1998) Genetic analysis of virulence in the rice blast fungus Magnaporthe grisea. Phytopathology 78:1227–1233CrossRefGoogle Scholar
  116. Levitz SM (1991) The ecology of Cryptococcus neoformans and the epidemiology of cryptococcosis. Rev Infect Dis 13:1163–1169PubMedCrossRefGoogle Scholar
  117. Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227:1435–1441PubMedCrossRefGoogle Scholar
  118. Lucas M, Gwillam R, Lepingle A, Rajndream MA et al.(2000) Sequence analysis of two cosmids from Schizosaccharomyces pombe chromosome III. Yeast 16:1519–1526PubMedCrossRefGoogle Scholar
  119. Machida M, Akita O, Kashiwagi Y, Koyarna Y, Yamaguchi S et al. (2000) Analyses of ESTs and the promoters of useful expression patterns from Aspergillus oryzae. Int Symp Mol Biol Filamentous Fungi Aspergilli, p 3 (Abstr)Google Scholar
  120. Magee BB, Magee PT (2000) Induction of mating in Candida albicans by construction of MTLa and MTLα strains. Science 289:310–313PubMedCrossRefGoogle Scholar
  121. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402:83–86PubMedCrossRefGoogle Scholar
  122. Maier E, Hoheisel JD, McCarthy LM, Mott R, Grigoriev AV et al. (1992) Complete coverage of the Schizosaccharomyces pombe genome in yeast artificial chromosomes. Nature Genet 1:273–277PubMedCrossRefGoogle Scholar
  123. Martzen MR et al. (1999) A biochemical genomics approach to identify genes by the activity of their products. Science 286:1153–1155PubMedCrossRefGoogle Scholar
  124. May GS, Adams TH (1997) The importance of fungi to man. Genome Res 7:1041–1044PubMedGoogle Scholar
  125. McClintock B (1945) Neurospora. 1. Preliminary observations of the chromosomes of Neurospora crassa. Am J Bot 32:671–678CrossRefGoogle Scholar
  126. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A et al. (1997) Overview of the yeast genome. Nature (Suppl) 387:7–8Google Scholar
  127. Mewes HW, Heumann K, Kaps A, Mayer K, Pfeiffer F et al. (1999) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 27:44–48PubMedCrossRefGoogle Scholar
  128. Minto RE, Townsend CA (1997) Enzymology and molecular biology of aflatoxin biosynthesis. Chem Rev 97: 2537–2555PubMedCrossRefGoogle Scholar
  129. Nelson MA, Kang S, Braun EL, Crawford ME, Dolan PL et al. (1997) Expressed sequences from conidial, mycelial and sexual stages of Neurospora crassa. Fungal Genet Biol 21:348–363PubMedCrossRefGoogle Scholar
  130. Nelson RT, Hua J, Pryor B, Lodge JK (2001) Identification of virulence mutants of the fungal pathogen, Crypto-coccus neoformans, using signature tagged mutagenesis. Genetics 157:935–947PubMedGoogle Scholar
  131. Nurse P (1994) Ordering S phase and M phase in the cell cycle. Cell 79:547–550PubMedCrossRefGoogle Scholar
  132. O’Brien SJ (ed) (1993) Genetic maps. Locus maps of complex genomes, vol 3. Lower eukaryotes. Cold Spring Harbor Press, Cold Spring HarborGoogle Scholar
  133. Oliver S (2000) Guilt-by-association goes global. Nature 403:601–603PubMedCrossRefGoogle Scholar
  134. Orbach MJ, Vollrath D, Davis RW, Yanofsky C (1988) An electrophoretic karyotype of Neurospora crassa. Mol Cell Biol 8:1469–1473PubMedGoogle Scholar
  135. Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837–846PubMedCrossRefGoogle Scholar
  136. Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 83:63–98CrossRefGoogle Scholar
  137. Pearson WR (1991) Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11:635–650PubMedCrossRefGoogle Scholar
  138. Pearson WR, Miller W (1992) Dynamic programming algorithms for biological sequence comparison. Methods Enzymol 210:575–601PubMedCrossRefGoogle Scholar
  139. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444–2448PubMedCrossRefGoogle Scholar
  140. Perkins DD, Radford A, Newmeyer D, Bjorkman M (1982) Chromosomal loci of Neurospora crassa. Microbiol Rev 46:426–570PubMedGoogle Scholar
  141. Perkins D, Radford A, Sachs M (2000) Compendium of chromosomal mutations of Neurospora. Academic Press, San DiegoGoogle Scholar
  142. Peruski LF, Peruski AH (1997) The Internet and the new biology, tools for genomic and molecular research. American Society of Microbiology Press, Washington, DCGoogle Scholar
  143. Pla J, Gil C, Monteoliva L, Navarro-Garcia F, Sanchez M, Nombela C (1996) Understanding Candida albicans at the molecular level. Yeast 12:1677–1702PubMedCrossRefGoogle Scholar
  144. Pontecorvo G (1956) The parasexual cycle in fungi. Annu Rev Microbiol 10:393–400PubMedCrossRefGoogle Scholar
  145. Pontecorvo G, Roper JA, Hemmons LM, Macdonald KD, Bufton AW J (1952) The genetics of Aspergillus nidulans. Adv Genet 5:141–238CrossRefGoogle Scholar
  146. Prade RA (1998) Meeting review. Fungal genomics — one per week. Fungal Genet Biol 25:76–78PubMedCrossRefGoogle Scholar
  147. Prade RA (2000) The reliability of the Aspergillus nidulans physical map. Fungal Genet Biol 29:175–185PubMedCrossRefGoogle Scholar
  148. Prade RA, Griffith J, Kochut K, Arnold J, Timberlake WE (1997) In vitro reconstruction of the Aspergillus (= Emericella) nidulans genome. Proc Natl Acad Sci USA 94:14564–14569PubMedCrossRefGoogle Scholar
  149. Prade RA, Ayoubi P, Misawa E, Garcia F, Ray T, Samad R et al. (2001a) Large-scale genome DNA sequence survey of the Aspergillus nidulans chromosome IV (in preparation)Google Scholar
  150. Prade RA, Ayoubi P, Krishnan S, Macwana S, Russell H (2001b) Accumulation of stress and cell wall degrading enzyme associated transcripts during asexual development in Aspergillus nidulans. Genetics 157:957–967PubMedGoogle Scholar
  151. Primrose SB (1995) Principles of genome analysis. Black-well Science, OxfordGoogle Scholar
  152. Qutob D, Graber P, Sobral B, Gijzen M (2000) Comparative analysis and expressed sequences in Phytophthora sojae. Plant Physiol 123:243–253PubMedCrossRefGoogle Scholar
  153. Raeder U, Thompson W, Broda P (1989) RLFP-based genetic maps of Phanerochaete chrysosporium ME44: lignin peroxidase genes occur in clusters. Mol Microbiol 3:911–918PubMedCrossRefGoogle Scholar
  154. Radford A, Parish JH (1997) The genome and genes of Neurospora crassa. Fungal Genet Biol 21:258–266PubMedCrossRefGoogle Scholar
  155. Romao J, Hamer JE (1992) Genetic organization of a repeated DNA sequence family in the rice blast fungus. Proc Natl Acad Sci USA 89:5316–5320PubMedCrossRefGoogle Scholar
  156. Randall TA, Judelson HS (1999) Construction of a bacterial artificial chromosome library of Phytophthora infestans and transformation of clones into P. infestans. Fungal Genet Biol 28:160–170PubMedCrossRefGoogle Scholar
  157. Rieder MJ, Taylor SL, Tobe VO, Nickerson DA (1998) Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Res 26:967–973PubMedCrossRefGoogle Scholar
  158. Riley M (1993) Functions of the gene products of Escherichia coli. Microbiol Rev 57:862–952PubMedGoogle Scholar
  159. Riley M, Serres MH (2000) Interim report on genomics of Escherichia coli. Annu Rev Microbiol 54:341–411PubMedCrossRefGoogle Scholar
  160. Rippon JW (1988) Medical mycology, the pathogenic fungi and the pathogenic actinomycetes, 3rd edn. WB Saunders, PhiladelphiaGoogle Scholar
  161. Rubin GM, Yandell MD, Wortman JR, Miklos GLG, Nelson CR et al. (2000) Comparative genomics of the eukaryotes. Science 287:2204–2220PubMedCrossRefGoogle Scholar
  162. Schatz BR (1997) Information retrieval in digital libraries: bringing search to the net. Science 275:327–334PubMedCrossRefGoogle Scholar
  163. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470PubMedCrossRefGoogle Scholar
  164. Scherer S, Magee PH (1990) Genetics of Candida albicans. Microbiol Rev 54:226–241PubMedGoogle Scholar
  165. Schulte U, Becker I, Mewes HW, Mannhaupt G (2001) Large scale analysis of sequences from Neurospora crassa. J Biotech (in press)Google Scholar
  166. Sebghati TS, Engle JT, Goldman WE (2000) Intracellular parasitism by Histoplasma capsulatum: ungal virulence and calcium dependence. Science 290:1968–1971CrossRefGoogle Scholar
  167. Service RF (2000) Can Celera do it again? Science 287:2136–2138PubMedCrossRefGoogle Scholar
  168. Sherman F (1981) Genetic nomenclature. In: Strathern JN, Jones EW, Broach JR (eds) Molecular Biology of the yeast Saccharomyces cerevisiae. Cold Spring Harbor Lab, Cold Spring Harbor, pp 639–640Google Scholar
  169. Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genet 14:450–456PubMedCrossRefGoogle Scholar
  170. Skinner DZ, Budde AD, Leong SA (1991) Molecular karyotype analysis of fungi. In: Bennett JW, Lasurel L (eds) More Gene Manipulations in Fungi. Academic Press, New York, pp 86–102CrossRefGoogle Scholar
  171. Skinner DZ, Budde AD, Farman ML, Leung H et al. (1993) Genome organization of the rice blast fungus, Magnaporthe grisea: genetic map, electrophoretic karyotype, and occurrence of repeated DNAs. Theor Appl Genet 87:545–557CrossRefGoogle Scholar
  172. Skolnick J, Fetrow JS, Kolinski A (2000) Structural genomics and its importance for gene function analysis. Nature Biotech 18:283–287CrossRefGoogle Scholar
  173. Smith JMB (1989) Opportunistic mycoses of man and other animals. CAB International, WallingfordGoogle Scholar
  174. Smulian AG, Sesterhenn T, Tanaka R, Cushion MT (2001) The ste3 pheromone receptor gene of the Pneumocystis carnii is surrounded by a cluster of signal transduction genes. Genetics 157:991–1002PubMedGoogle Scholar
  175. Stebbins GL (1966) Chromosome variation and evolution. Science 152:1463–1469PubMedCrossRefGoogle Scholar
  176. Sunkin SM, Stringer JR (1996) Translocation of surface antigen genes to a unique telomeric site in Pneumocystis carinii. Mol Microbiol 19:283–295PubMedCrossRefGoogle Scholar
  177. Sweigard JA, Valent B, Orbach MJ, Walter AM, Rafalski A et al. (1993) Genetic map of the rice blast fungus Magnaporthe grisea (n = 7). In: O’Brien SJ (ed) Genetics Maps, 6th edn. Cold Spring Harbor Lab Press, Cold Spring Harbor, pp 3.112–3.114Google Scholar
  178. Sweigard JA, Carrol A, Kang S, Farrall L, Chumley FC et al. (1995) Identification, cloning and characterization of PWL2, a gene for host species specificity in the rice blast fungus. Plant Cell 7:1221–1233PubMedGoogle Scholar
  179. Swindell SR, Miller RR, Myers GAS (eds) (1995) Internet for the molecular biologist. Horizon Sci Press, NorfolkGoogle Scholar
  180. Sybenga J (1972) General cytogenetics. Am Elsevier Publ, New YorkGoogle Scholar
  181. Tait E, Simon MC, King S, Brown AJ, Gow NAR et al. (1997) A Candida albicans genome project: cosmid contigs, physical mapping, and gene isolation. Fungal Genet Biol 21:308–314PubMedCrossRefGoogle Scholar
  182. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631–637PubMedCrossRefGoogle Scholar
  183. Taylor JW, Hass T, Kerp H (1999) The oldest fossil ascomycetes. Nature 399:648PubMedCrossRefGoogle Scholar
  184. Thompson KA (1999) Useful informatics for industrial microbiologists. Soc Ind Microbiol News 49:5–10Google Scholar
  185. Timberlake WE (1990) Molecular genetics of Aspergillus development. Annu Rev Genet 24:5–36PubMedCrossRefGoogle Scholar
  186. Timberlake WE (1991) Cloning and analysis of fungal genes. In: Bennett JW, Lasure LL (eds) More gene manipulations in fungi. Academic Press, San Diego, pp 51–85CrossRefGoogle Scholar
  187. Tobin MB, Peery RB, Skatrud PL (1997) An electrophoretic molecular karyotype of a clinical isolate of Aspergillus fumigatus and localization of the MDR-like genes AfuMDRl and AfuMDR2. Diagn Microbiol Infect Dis 29:67–71PubMedCrossRefGoogle Scholar
  188. Tooley PW, Carras MM (1992) Separation of chromosomes of Phytophthora species using CHEF gel electrophoresis. Exp Mycol 16:188–196CrossRefGoogle Scholar
  189. Tooley PW, Therrein CD (1987) Cytophotometric determination of the nuclear DNA content of 23 Mexican and 18 non-Mexican isolates of Phytophthora infestans. Exp Mycol 11:19–26CrossRefGoogle Scholar
  190. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623–627PubMedCrossRefGoogle Scholar
  191. Van der Lee T, De Witte I, Drenth A, Alfonso C, Govers F (1997) AFLP linkage map of the oomycete Phytophthora infestans. Fungal Genet Biol 21:278–291PubMedCrossRefGoogle Scholar
  192. Van der Lee T, Robold A, Testa A, Van’t Klooster JW, Govers F (2001) Mapping of avirulance genes in Phytophthora infestans with AFLP markers selected by bulked segregant analysis. Genetics 157:949–956PubMedGoogle Scholar
  193. Venter JC, Smith HO, Hood L (1996) A new strategy for genome sequencing. Nature 381:364–366PubMedCrossRefGoogle Scholar
  194. Venter JC, Adams MD, Sutton GG, Kerlavage AR, Smith HO, Hunkapiller M (1998) Shotgun sequencing of the human genome. Science 280:1540–1542PubMedCrossRefGoogle Scholar
  195. Venter JC, Adams MD, Myers EW et al. (2001) The sequence of the human genome. Science 291:1304–1351PubMedCrossRefGoogle Scholar
  196. Verdoes JC, Calil MR, Punt PJ, Debets F, Swart K et al.(1994) The complete karyotype of Aspergillus niger: the use of introduced electrophoretic mobility variation of chromosomes for gene assignment studies. Mol Gen Genet 244:75–80PubMedCrossRefGoogle Scholar
  197. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  198. Walz M (1995) Electrophoretic karyotyping. In: Kück U (ed) Genetics and biotechnology, vol 2. The Mycota. Springer, Berlin Heidelberg New York, pp 63–73Google Scholar
  199. Watson AJ, Fuller LJ, Jeenes DJ, Archer DB (1999) Homologs of aflatoxin biosynthesis genes and sequence of aflR in Aspergillus oryzae and Aspergillus sojae. Appl Environ Microbiol 65:307–310PubMedGoogle Scholar
  200. Waugh M, Hraber P, Weiler J, Wu Y, Chen G et al. (2000) The Phytophthora genome initiative database: informatics and analysis for distributed pathogenic research. Nucleic Acids Res 28:87–94PubMedCrossRefGoogle Scholar
  201. Weidner G, d’Enfert C, Koch A, Mop PC, Brakhage AA (1998) Development of a homologous transformation system for the human pathogenic fungus Aspergillus fumigatus based on the PyrG gene encoding orotidine 5′-monophosphate decarboxylase. Curr Genet 33: 378–385PubMedCrossRefGoogle Scholar
  202. Wendland J, Ayad-Durieux Y, Knechtle P, Rebischung R, Philippsen P (2000) PCR-based gene targeting in the filamentous fungus Ashbya gossypii. Gene 242:381–392PubMedCrossRefGoogle Scholar
  203. Whelan WL (1987) The genetics of medically important fungi. Crit Rev Microbiol 14:99–170PubMedCrossRefGoogle Scholar
  204. Whelan WL, Kwon-Chung KJ (1986) Genetic complementation in Cryptococcus neoformans. J Bacteriol 16:924–928Google Scholar
  205. Woloshuk CP, Prieto R (1998) Genetic organization and function of the aflatoxin B1 biosynthetic genes. FEMS Microbiol Lett 160:169–176PubMedCrossRefGoogle Scholar
  206. Xiang Z, Moore K, Wood V, Rajandream MA, Barrell BG et al. (2000) Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromeredistal to his5. Yeast 16:1405–1411PubMedCrossRefGoogle Scholar
  207. Xiong M, Chen HJ, Prade RA, Wang Y, Griffith J, Timberlake WE, Arnold J (1996) On the consistency of physical mapping method to reconstruct a chromosome in vitro. Genetics 142:267–284PubMedGoogle Scholar
  208. Young RA (2000) Biomedical discovery with DNA arrays. Cell 102:9–15PubMedCrossRefGoogle Scholar
  209. Yuan G-F, Liu C-S, Chen C-C (1995) Differentiation of Aspergillus parasiticus from Aspergillus sojae by random amplification of polymorphic DNA. Appl Environ Microbiol 61:2384–2387PubMedGoogle Scholar
  210. Zhu H, Choi S, Toleston AT, Wing RA, Dean RA (1997) A large-insert (130 Kbp) bacterial artificial chromosome library of the virublast fungus Magnaporthe grisea: genome analysis, configuration, assembly, and gene cloning. Fungal Genet Biol 21:337–347PubMedCrossRefGoogle Scholar
  211. Zhu H, Nowrousian M, Kupfer D, Colot HV, Berrocaltito G et al. (2001) Analysis of ESTs from two starvation, time of day-specific libraries of Neurospora crassa reveals novel clock-controlled genes. Genetics 157:1057–1065PubMedGoogle Scholar
  212. Zolan ME (1995) Chromosome-length polymorphisms in fungi. Microbiol Rev 59:686–698PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • J. W. Bennett
    • 1
  • Jonathan Arnold
    • 2
  1. 1.Department of Cell and Molecular BiologyTulane UniversityNew OrleansUSA
  2. 2.Department of GeneticsUniversity of GeorgiaAthensUSA

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