Functional & Integrative Genomics

, Volume 4, Issue 4, pp 207–218 | Cite as

A comparative genomic analysis of ESTs from Ustilago maydis

  • Ryan Austin
  • Nicholas J. Provart
  • Nuno T. Sacadura
  • Kimberly G. Nugent
  • Mohan Babu
  • Barry J. Saville
Original Paper


A large-scale comparative genomic analysis of unisequence sets obtained from an Ustilago maydis EST collection was performed against publicly available EST and genomic sequence datasets from 21 species. We annotated 70% of the collection based on similarity to known sequences and recognized protein signatures. Distinct grouping of the ESTs, defined by the presence or absence of similar sequences in the species examined, allowed the identification of U. maydis sequences present only (1) in fungal species, (2) in plants but not animals, (3) in animals but not plants, or (4) in all three eukaryotic lineages assessed. We also identified 215 U. maydis genes that are found in the ascomycete but not in the basidiomycete genome sequences searched. Candidate genes were identified for further functional characterization. These include 167 basidiomycete-specific sequences, 58 fungal pathogen-specific sequences (including 37 basidiomycete pathogen-specific sequences), and 18 plant pathogen-specific sequences, as well as two sequences present only in other plant pathogen and plant species.


Fungal comparative genomics EST analysis Ustilago maydis 



We would like to acknowledge the assistance of Kristen Choffe in the creation of cDNA libraries and sequencing. Funding provided by NSERC Canada to B. J. Saville.


  1. Agrios GN (1997) Plant pathology, 4th edn. San Diego Academic, San DiegoGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedGoogle Scholar
  4. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, et al (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29:37–40CrossRefPubMedGoogle Scholar
  5. Banuett F (1995) Genetics of Ustilago maydis, a fungal pathogen that induces tumors in maize. Annu Rev Genet 29:179–208CrossRefPubMedGoogle Scholar
  6. Banuett F, Herskowitz I (1989) Different a alleles of Ustilago maydis are necessary for maintenance of filamentous growth but not for meiosis. Proc Natl Acad Sci USA 86:5878–5882Google Scholar
  7. Boguski MS, Tolstoshev CM, Bassett DE Jr (1994) Gene discovery in dbEST. Science 265:1993–1994PubMedGoogle Scholar
  8. Braun EL, Halpern AL, Nelson MA, Natvig DO (2000) Large-scale comparison of fungal sequences information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res 10:416–430CrossRefPubMedGoogle Scholar
  9. Deeks MJ, Hussy PJ, Davies B (2002) Formins: intermediates in signal-transduction cascades that affect cyskeletal reorganization. Trends Plant Sci 7:492–498CrossRefPubMedGoogle Scholar
  10. Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14:307–311CrossRefPubMedGoogle Scholar
  11. Graveley BR (2000) Sorting out the complexity of SR protein functions. RNA 6:1197–1211CrossRefPubMedGoogle Scholar
  12. Henikoff S, Henikoff J (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915–10919PubMedGoogle Scholar
  13. Hoffmann T, Golz C, Schieder O (1994) Foreign DNA sequences are received by a wild-type strain of Aspergillus niger after co-culture with transgenic higher plants. Curr Genet 27:70–76PubMedGoogle Scholar
  14. Holst-Jensen A, Vaage M, Schumacher T, Johansen S (1999) Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi. Mol Biol Evol 16:114–126PubMedGoogle Scholar
  15. Kamoun S, Hraber P, Sobral B, Nuss D, Govers F (1999) Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences. Fungal Genet Biol 28:94–106CrossRefPubMedGoogle Scholar
  16. Kämper J, Weinzierl G, Brachmann A, Feldbrügge M, Basse C, Steinberg G, Kahmann R, Friedrich G, Vollenbroich V, Koopmann E, et al (2001) The Ustilago maydis sequencing project. Fungal Genet Newsl 48 [Suppl]:500Google Scholar
  17. Karlsson M, Olson A, Stenlid J (2003) Expressed sequences from the basidiomycetous tree pathogen Heterobasidion annosum during early infection of scots pine. Fungal Genet Biol 39:51–59CrossRefPubMedGoogle Scholar
  18. Kay BK, Williamson MP, Sudol M (2000) The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J 14:231–241PubMedGoogle Scholar
  19. Keogh RS, Seoighe C, Wolfe KH (1998) Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast 14:443–457CrossRefPubMedGoogle Scholar
  20. Keon J, Bailey A, Hargreaves J (2000) A group of expressed cDNA sequences from the wheat fungal leaf blotch pathogen, Mycosphaerella graminicola (Septoria tritici). Fungal Genet Biol 29:118–133CrossRefPubMedGoogle Scholar
  21. Kim S, Ahn IP, Lee YH (2001) Analysis of genes expressed during rice–Magnaporthe grisea interactions. Mol Plant Microbe Interact 14:1340–1346PubMedGoogle Scholar
  22. Kocks C (1994) Intracellular motility. Profilin puts pathogens on the actin drive. Curr Biol 4:465–468CrossRefPubMedGoogle Scholar
  23. Kruger WM, Pritsch C, Chao S, Muehlbauer GJ (2002) Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum. Mol Plant Microbe Interact 15:445–455PubMedGoogle Scholar
  24. Lai MC, Kuo HW, Chang WC, Tarn WY (2003) A novel splicing regulator shares a nuclear import pathway with SR proteins. EMBO J 22:1359–1369CrossRefPubMedGoogle Scholar
  25. Ma L, Galagan J, Calvo S, Nielsen C, Elkins T, Barrett R, Wong M, Lander E, Nusbaum C, Birren B (2003) The fungal genome initiative. Fungal Genet Newsl 50 [Suppl]:300Google Scholar
  26. Martinez-Espinoza AD, Garcia-Pedrajas MD, Gold SE (2002) The Ustilaginales as plant pests and model systems. Fungal Genet Biol 35:1–20CrossRefPubMedGoogle Scholar
  27. Mata J, Bahler J (2003) Correlations between gene expression and gene conservation in fission yeast. Genome Res 13:2686–2690CrossRefPubMedGoogle Scholar
  28. Matthews JM, Sunde M (2002) Zinc fingers-folds for many occasions. IUBMB Life 54(6):351–355CrossRefPubMedGoogle Scholar
  29. Mount DW (2001) Bioinformatics: sequence and genome analysis. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 495–497Google Scholar
  30. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, et al (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31:315–318CrossRefPubMedGoogle Scholar
  31. Neumann MJ, Dobinson KF (2003) Sequence tag analysis of gene expression during pathogenic growth and microsclerotia development in the vascular wilt pathogen Verticillium dahliae. Fungal Genet Biol 38:54–62CrossRefPubMedGoogle Scholar
  32. Nugent KG, Choffe K, Saville BJ (2004) Gene expression during Ustilago maydis diploid filamentous growth: EST library creation and analyses. Fungal Genet Biol 41(3):349–360CrossRefPubMedGoogle Scholar
  33. Pelletier R, Krasilnikova MM, Samadashwily GM, Lahue R, Mirkin SM (2003) Replication and expansion of trinucleotide repeats in yeast. Mol Cell Biol 23:1349–1357CrossRefPubMedGoogle Scholar
  34. Provart N, Zhu T (2003) A browser-based functional classification SuperViewer for Arabidopsis genomics. Curr Comput Mol Biol 2003:271–272Google Scholar
  35. Qutob D, Hraber PT, Sobral BW, Gijzen M (2000) Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiol 123:243–254CrossRefPubMedGoogle Scholar
  36. Rosewich UL, Kistler HC (2000) Role of horizontal gene transfer in the evolution of fungi. Annu Rev Phytopathol 38:325–363CrossRefPubMedGoogle Scholar
  37. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al (2000) Comparative genomics of the eukaryotes. Science 287:2204–2215CrossRefPubMedGoogle Scholar
  38. Sacadura NT, Saville BJ (2003) Gene expression and EST analyses of Ustilago maydis germinating teliospores. Fungal Genet Biol 40(1):47–64CrossRefPubMedGoogle Scholar
  39. Saville BJ, Leong SA (1992) The molecular biology of pathogenesis in Ustilago maydis. In: Setlow JK (ed) Genetic engineering: principles and methods, vol 14. Plenum, New YorkGoogle Scholar
  40. Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, et al (2000) Prevalence of small inversions in yeast gene order evolution. Proc Natl Acad Sci USA 97:14433–14437CrossRefPubMedGoogle Scholar
  41. Skinner W, Keon J, Hargreaves J (2001) Gene information for fungal pathogens from expressed sequences. Curr Opin Microbiol 4:381–386CrossRefPubMedGoogle Scholar
  42. Soanes DM, Skinner W, Keon J, Hargreaves J, Talbot NJ (2002) Genomics of phytopathogenic fungi and the development of bioinformatic resources. Mol Plant Microbe Interact 15:421–427PubMedGoogle Scholar
  43. Swann EC, Taylor JW (1993) Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia 85:923–936Google Scholar
  44. Thomas SW, Rasmussen SW, Glaring MA, Rouster JA, Christiansen SK, Oliver RP (2001) Gene identification in the obligate fungal pathogen Blumeria graminis by expressed sequence tag analysis. Fungal Genet Biol 33:195–211CrossRefPubMedGoogle Scholar
  45. Trail F, Xu J, San Miguel P, Halgren RG, Corby Kistler H (2003) Analysis of expressed sequence tags from Gibberella zeae (anamorph Fusarium graminearum). Fungal Genet Biol 38:187–197CrossRefPubMedGoogle Scholar
  46. Vaughn JC, Mason MT, Sper-Whitis GL, Kulman P, Palmer JD (1995) Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric coxI gene of Peperomia. J Mol Evol 41:563–572PubMedGoogle Scholar
  47. Walker DR, Koonin EV (1997) SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol 5:333–339PubMedGoogle Scholar
  48. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708–713CrossRefPubMedGoogle Scholar
  49. Wolven AK, Belmont LD, Mahoney NM, Almo SC, Drubin DG (2000) In vivo importance of actin nucleotide exchange catalyzed by profilin. J Cell Biol 150:895–904CrossRefPubMedGoogle Scholar
  50. Yoder OC, Turgeon BG (2001) Fungal genomics and pathogenicity. Curr Opin Plant Biol 4:315–321CrossRefPubMedGoogle Scholar
  51. Zdobnov EM, Apweiler R (2001) InterProScan: an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Ryan Austin
    • 1
  • Nicholas J. Provart
    • 1
  • Nuno T. Sacadura
    • 2
  • Kimberly G. Nugent
    • 2
  • Mohan Babu
    • 2
  • Barry J. Saville
    • 2
  1. 1.Department of BotanyUniversity of TorontoTorontoCanada
  2. 2.Department of BotanyUniversity of Toronto at MississaugaMississaugaCanada

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