Molecular Genetics and Genomics

, Volume 276, Issue 1, pp 87–100

Microarray analysis of transcript accumulation during perithecium development in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum)

Original Paper


Gibberella zeae (anamorph Fusarium graminearum) is the causal agent of Fusarium head blight (FHB) of wheat and barley in the United States. Ascospores forcibly discharged from mature fruiting bodies, the perithecia, serve as the primary inoculum for FHB epidemics. To identify genes important for perithecium development and function, a cDNA microarray that covered 11% of the G. zeae genome was constructed. The microarray was used to measure changes in transcription levels of genes expressed during three successive stages of perithecium development. When compared with vegetative mycelia, 651 (31%) cDNA clones showed changes in transcript levels in at least one of the three developmental stages. During perithecium development, 263 (13%) cDNA clones showed temporal changes in transcript profiles. Transcripts that showed the greatest changes in levels in maturing perithecia belonged to genes in the FunCat main functional categories of cell rescue, metabolism, cell type differentiation, energy, and cellular transport. For genes related to metabolism and cell type differentiation, transcripts showed the highest levels in immature perithecia, whereas for cellular transport-related genes, transcripts showed the highest levels in mature perithecia. This study represents the first large-scale investigation of both spatial and temporal changes in transcript levels during perithecium development. It provides clear evidence that the sexual development in fungi is a complex, multigenic process and identifies genes involved in sexual development of this agriculturally important fungus.


Gibberella zeae Fusarium graminearum Perithecia Sexual development cDNA microarray Transcript accumulation 

Supplementary material


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. Beemster GTS, De Veylder L, Vercruysse S, West G, Rombaut D, Van Hummelen P, Galichet A, Gruissem W, Inze D, Vuylsteke M (2005) Genome-wide analysis of gene expression profiles associated with cell cycle transitions in growing organs of Arabidopsis. Plant Physiol 138:734–743PubMedCrossRefGoogle Scholar
  3. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O’Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 68:1–108PubMedCrossRefGoogle Scholar
  4. Bowman EJ, Kendle R, Bowman BJ (2000) Disruption of vma-1, the gene encoding the catalytic subunit of the vacuolar H+-ATPase, causes severe morphological changes in Neurospora crassa. J Biol Chem 275:167–176PubMedCrossRefGoogle Scholar
  5. Brown DW, McCormick SP, Alexander NJ, Proctor RH, Desjardins AE (2001) A genetic and biochemical approach to study trichothecene diversity in Fusarium sporotrichioides and Fusarium graminearum. Fungal Genet Biol 32:121–133PubMedCrossRefGoogle Scholar
  6. Calvo AM, Gardner HW, Keller NP (2001) Genetic connection between fatty acid metabolism and sporulation in Aspergillus nidulans. J Biol Chem 276:25766–25774PubMedCrossRefGoogle Scholar
  7. Chang PK, Wilson RA, Keller NP, Cleveland TE (2004) Deletion of the 12-oleic acid desaturase gene of a nonaflatoxigenic Aspergillus parasiticus field isolate affects conidiation and sclerotial development. J Appl Microbiol 97:1178–1184PubMedCrossRefGoogle Scholar
  8. Chuaqui RF, Bonner RF, Best CJM, Gillespie JW, Flaig MJ, Hewitt SM, Phillips JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V, Emmert-Buck MR (2002) Post-analysis follow-up and validation of microarray experiments. Nat Genet 32:509–514PubMedCrossRefGoogle Scholar
  9. Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32(Suppl):490–496PubMedCrossRefGoogle Scholar
  10. Coppin E, Debuchy R, Arnaise S, Picard M (1997) Mating types and sexual development in filamentous ascomycetes. Microbiol Mol Biol Rev 61:411–428PubMedGoogle Scholar
  11. Cui X, Churchill G (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4:210PubMedCrossRefGoogle Scholar
  12. DeLange AM, Griffiths AJF (1980) Meiosis in Neurospora crassa. I. The isolation of recessive mutants defective in the production of viable ascospores. Genetics 96:367–378PubMedGoogle Scholar
  13. Desjardins AE, Brown DW, Yun SH, Proctor RH, Lee T, Plattner RD, Lu SW, Turgeon BG (2004) Deletion and complementation of the mating type (MAT) locus of the wheat head blight pathogen Gibberella zeae. Appl Environ Microbiol 70:2437–2444PubMedCrossRefGoogle Scholar
  14. Dong H, Wade M, Williams A, Lee A, Douglas GR, Yauk C (2005) Molecular insight into the effects of hypothyroidism on the developing cerebellum. Biochem Biophys Res Commun 330:1182–1193PubMedCrossRefGoogle Scholar
  15. Duarte M, Videira A (2000) Respiratory chain complex I is essential for sexual development in Neurospora and binding of iron sulfur clusters are required for enzyme assembly. Genetics 156:607–615PubMedGoogle Scholar
  16. Dubin HJ, Gilchrist L, Reeves J, McNab A (1997) Fusarium head scab: global status and prospects. CIMMYT, Mexico CityGoogle Scholar
  17. Eckert SE, Hoffmann B, Wanke C, Braus GH (1999) Sexual development of Aspergillus nidulans in tryptophan auxotrophic strains. Arch Microbiol 172:157–166PubMedCrossRefGoogle Scholar
  18. Eckert SE, Kubler E, Hoffmann B, Braus GH (2000) The tryptophan synthase-encoding trpB gene of Aspergillus nidulans is regulated by the cross-pathway control system. Mol Gen Genet 263:867–876PubMedCrossRefGoogle Scholar
  19. Everitt BS (1977) The analysis of contingency tables. Chapman and Hall, LondonGoogle Scholar
  20. Fischer R, Kues U (2003) Developmental processes in filamentous fungi. In: Bennett JW, Lemke PA (eds) Mycology series. Dekker, New York, pp 41–118Google Scholar
  21. Gaffoor I, Trail F (2006) Characterization of two polyketide synthase genes involved in zearalenone biosynthesis in Gibberella zeae. Appl Environ Microbiol 72:1793–1799PubMedCrossRefGoogle Scholar
  22. Gao H, Wang Y, Liu X, Yan T, Wu L, Alm E, Arkin A, Thompson DK, Zhou J (2004) Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol 186:7796–7803PubMedCrossRefGoogle Scholar
  23. Glass NL, Grotelueschen J, Metzenberg RL (1990) Neurospora crassa a mating-type region. Proc Natl Acad Sci USA 87:4912–4916PubMedCrossRefGoogle Scholar
  24. Goodrich-Tanrikulu M, Howe K, Stafford A, Nelson MA (1998) Changes in fatty acid composition of Neurospora crassa accompany sexual development and ascospore germination. Microbiology 144:1713–1720PubMedCrossRefGoogle Scholar
  25. Goodrich-Tanrikulu M, Jacobson DJ, Stafford AE, Lin J-T, McKeon TA (1999) Characterization of Neurospora crassa mutants isolated following repeat-induced point mutation of the beta subunit of fatty acid synthase. Curr Genet 36:147–152PubMedCrossRefGoogle Scholar
  26. Guenther J, Trail F (2005) The development and differentiation of Gibberella zeae (anamorph: Fusarium graminearum) during colonization of wheat. Mycologia 97:232–240CrossRefGoogle Scholar
  27. Güldener U, Mannhaupt G, Munsterkotter M, Haase D, Oesterheld M, Stumpflen V, Mewes H-W, Adam G (2006a) FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. Nucleic Acids Res 34:D456–D458CrossRefGoogle Scholar
  28. Güldener U, Seong KY, Boddu J, Cho S, Trail F, Xu JR, Adam G, Mewes HW, Muehlbauer GJ, Kistler HC (2006b) Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta. Fungal Genet Biol 43:316–325CrossRefGoogle Scholar
  29. Han YK, Lee T, Han KH, Yun SH, Lee J (2004) Functional analysis of the homoserine O-acetyltransferase gene and its identification as a selectable marker in Gibberella zeae. Curr Genet 46:205–212PubMedCrossRefGoogle Scholar
  30. Helmann JD, Wu MFW, Kobel PA, Gamo FJ, Wilson M, Morshedi MM, Navre M, Paddon C (2001) Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 183:7318–7328PubMedCrossRefGoogle Scholar
  31. Heyer LJ, Kruglyak S, Yooseph S (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res 9:1106–1115PubMedCrossRefGoogle Scholar
  32. Ivey FD, Hodge PN, Turner GE, Borkovich KA (1996) The G alpha i homologue gna-1 controls multiple differentiation pathways in Neurospora crassa. Mol Biol Cell 7:1283–1297PubMedGoogle Scholar
  33. Johnson TE (1979) A Neurospora mutation that arrests perithecial developmental as either male or female parent. Genetics 92:1107–1120PubMedGoogle Scholar
  34. Kerr MK, Churchill GA (2001) Experimental design for gene expression microarrays. Biostatistics 2:183–201PubMedCrossRefGoogle Scholar
  35. Kim H, Nelson MA (2005) Molecular and functional analyses of poi-2, a novel gene highly expressed in sexual and perithecial tissues of Neurospora crassa. Eukaryot Cell 4:900–910PubMedCrossRefGoogle Scholar
  36. Kim H, Metzenberg RL, Nelson MA (2002) Multiple functions of mfa-1, a putative pheromone precursor gene of Neurospora crassa. Eukaryot Cell 1:987–999PubMedCrossRefGoogle Scholar
  37. Kim Y-T, Lee Y-R, Jin J, Han K-H, Kim H, Kim J-C, Lee T, Yun Su-H, Lee Y-W (2005) Two different polyketide synthase genes are required for synthesis of zearalenone in Gibberella zeae. Mol Microbiol 58:1102–1113PubMedCrossRefGoogle Scholar
  38. Klittich C, Leslie JF (1988) Nitrate reduction mutants of Fusarium moniliforme (Gibberella fujikuroi). Genetics 118:417–423PubMedGoogle Scholar
  39. Kuldau GA, Raju NB, Glass NL (1998) Repeat-induced point mutations in Pad-1, a putative RNA splicing factor from Neurospora crassa, confer dominant lethal effects on ascus development. Fungal Genet Biol 23:169–180PubMedCrossRefGoogle Scholar
  40. Kuromori T, Yamamoto M (1994) Cloning of cDNAs from Arabidopsis thaliana that encode putative protein phosphatase 2C and a human Dr1-like protein by transformation of a fission yeast mutant. Nucleic Acids Res 22:5296–5301PubMedCrossRefGoogle Scholar
  41. Lee DW, Pratt RJ, McLaughlin M, Aramayo R (2003a) An argonaute-like protein is required for meiotic silencing. Genetics 164:821–828Google Scholar
  42. Lee J, Lee T, Lee Y-W, Yun S-H, Turgeon BG (2003b) Shifting fungal reproductive mode by manipulation of mating type genes: obligatory heterothallism of Gibberella zeae. Mol Microbiol 50:145–152CrossRefGoogle Scholar
  43. Leslie JF, Raju NB (1985) Recessive mutations from natural populations of Neurospora crassa that are expressed in the sexual diplophase. Genetics 111:759–777PubMedGoogle Scholar
  44. Losel DM, Sancholle M (1996) Fungal lipids. In: Prasad R, Ghannoum MA (eds) Lipids of pathogenic fungi. GRG Press, Boca Raton, pp 27–62Google Scholar
  45. Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J, Ruepp A (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 32:D41–D44PubMedCrossRefGoogle Scholar
  46. Mikheeva S, Barrier M, Little SA, Beyer R, Mikheev AM, Kerr MK, Mirkes PE (2004) Alterations in gene expression induced in day-9 mouse embryos exposed to Hyperthermia (HS) or 4-Hydroperoxycyclophosphamide (4CP): analysis using cDNA microarrays. Toxicol Sci 79:345–359PubMedCrossRefGoogle Scholar
  47. Minami K, Maniratanachote R, Katoh M, Nakajima M, Yokoi T (2006) Simultaneous measurement of gene expression for hepatotoxicity in thioacetamide-administered rats by DNA microarrays. Mutat Res 603:64–73PubMedGoogle Scholar
  48. Nelson MA, Merino ST, Metzenberg RL (1997) A putative rhamnogalacturonase required for sexual development of Neurospora crassa. Genetics 146:531–540PubMedGoogle Scholar
  49. Nowrousian M, Ringelberg C, Dunlap JC, Loros JJ, Kück U (2005) Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora. Mol Genet Genomics 273:137–149PubMedCrossRefGoogle Scholar
  50. Orr WC, Timberlake WE (1982) Clustering of spore-specific genes in Aspergillus nidulans. Proc Natl Acad Sci USA 79:5976–5980PubMedCrossRefGoogle Scholar
  51. Parguey-Leduc A, Janex-Favre MC (1981) Ascocarps of ascohymenial Pyrenomycetes. In: Reynolds DR (ed) Ascomycete systematics: the Luttrellian concept. Springer, Berlin Heidelberg New York, pp 102–123Google Scholar
  52. Pereya S, Dill-Macky R, Sims A (2004) Survival and inoculum production of Gibberella zeae in wheat residue. Plant Dis 88:724–730CrossRefGoogle Scholar
  53. Perkins DD, Radford A, Sachs MS (2001) The Neurospora compendium: chromosomal loci. Academic, San DiegoGoogle Scholar
  54. Rajeevan MS, Vernon SD, Taysavang N, Unger ER (2001) Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J Mol Diagn 3:26–31PubMedGoogle Scholar
  55. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes HW (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32:5539–5545PubMedCrossRefGoogle Scholar
  56. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34:374–378PubMedGoogle Scholar
  57. Sambrook J, Russell DG (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  58. Shaner G (2003) Epidemiology of Fusarium head blight of small grain cereals in North America. In: Leonard KJ, Bushnell WR (eds) Fusarium head blight of wheat and barley. APS Press, St Paul, pp 84–119Google Scholar
  59. Shrode LB, Lewis ZA, White LD, Bell-Pedersen D, Ebbole DJ (2001) vvd is required for light adaptation of conidiation-specific genes of Neurospora crassa, but not circadian conidiation. Fungal Genet Biol 32:169–181PubMedCrossRefGoogle Scholar
  60. Souza CA, Silva CC, Ferreira AV (2003) Sex in fungi: lessons of gene regulation. Genet Mol Res 2:136–147PubMedGoogle Scholar
  61. Stintzi A (2003) Gene expression profile of Campylobacter jejuni in response to growth temperature variation. J Bacteriol 185:2009–2016PubMedCrossRefGoogle Scholar
  62. Tan Y, Dragovic Z, Roenneberg T, Merrow M (2004) Entrainment dissociates transcription and translation of a circadian clock gene in Neurospora. Curr Biol 14:433–438PubMedCrossRefGoogle Scholar
  63. Trail F, Common R (2000) Perithecial development by Gibberella zeae: a light microscopy study. Mycologia 92:130–138CrossRefGoogle Scholar
  64. Trail F, Xu H, Loranger R, Gadoury D (2002) Physiological and environmental aspects of ascospore discharge in Gibberella zeae (anamorph Fusarium graminearum). Mycologia 94:181–189CrossRefGoogle Scholar
  65. Trail F, Xu J-R, Miguel PS, Halgren RG, Corby Kistler H (2003) Analysis of expressed sequence tags from Gibberella zeae (anamorph Fusarium graminearum). Fungal Genet Biol 38:187–197PubMedCrossRefGoogle Scholar
  66. Trail F, Gaffoor I, Vogel S (2005) Ejection mechanics and trajectory of the ascospores of Gibberella zeae (anamorph Fuarium graminearum). Fungal Genet Biol 42:528–533PubMedCrossRefGoogle Scholar
  67. Tsitsigiannis DI, Kowieski TM, Zarnowski R, Keller NP (2005) Three putative oxylipin biosynthetic genes integrate sexual and asexual development in Aspergillus nidulans. Microbiology 151:1809–1821PubMedCrossRefGoogle Scholar
  68. Woo Y, Krueger W, Kaur A, Churchill G (2005) Experimental design for three-color and four-color gene expression microarrays. Bioinformatics 21:i459–i467PubMedCrossRefGoogle Scholar
  69. Wu H, Kerr MK, Cui XQ, Churchill GA (2003) MAANOVA: a software package for the analysis of spotted cDNA microarray experiments. In: Parmigiani G, Garret ES, Irizarry RA, Zeger SL (eds) Analysis of gene expression data methods and software. Springer, Berlin Heidelberg New York, pp 313–431CrossRefGoogle Scholar
  70. Wurmbach E, Yuen T, Ebersole BJ, Sealfon SC (2001) Gonadotropin-releasing hormone receptor-coupled gene network organization. J Biol Chem 276:47195–47201PubMedCrossRefGoogle Scholar
  71. Young AN, Amin MB, Moreno CS, Lim SD, Cohen C, Petros JA, Marshall FF, Neish AS (2001) Expression profiling of renal epithelial neoplasms: a method for tumor classification and discovery of diagnostic molecular markers. Am J Pathol 158:1639–1651PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.Department of Plant BiologyMichigan State UniversityEast LansingUSA
  2. 2.National Food Safety and Toxicology CenterMichigan State UniversityEast LansingUSA
  3. 3.Department of Plant PathologyMichigan State UniversityEast LansingUSA

Personalised recommendations