Skip to main content
SpringerLink
Log in

Ustilago maydis transcript features identified through full-length cDNA analysis

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Ustilago maydis is the model for investigating basidiomycete biotrophic plant pathogens. To further the annotation of its genome, 12,943 full-length cDNA sequences were used to construct databases for the promoter and untranslated regions of U. maydis genes. A subset of clones was sequenced to determine full cDNA sequences. These and the original ESTs were assembled into contigs representing 3,058, or 45%, of the predicted U. maydis genes. The new sequencing allowed the confirmation of 2,842 gene models, 690 of which contain an intron. The use of full-length cDNA clone sequences ensured that untranslated regions were physically linked to the open reading frames (ORFs), not merely aligned upstream of the start of transcription. Identified sequence features include: (1) over 500 potential short upstream ORFs, (2) 95 gene models that require further annotation, (3) one new potential ORF, (4) varying GC content in different gene regions, (5) a WebLogo motif for the start of translation, (6) the correlation of UTR length with transcript representation in cDNA libraries and with gene function categories, (7) a relationship between natural antisense transcripts and UTR length that differs from that of Saccharomyces cerevisiae, (8) a potential relationship between DNA replication and the control of transcription, and (9) new insights regarding mechanisms for the control of transcription and mRNA maturation in U. maydis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB, Feldmann KA (2009) Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 69(1–2):179–194

    Article  PubMed  CAS  Google Scholar 

  • Allison LA (2007) Fundamental molecular biology. Blackwell, Malden

    Google Scholar 

  • 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(21):11319–11324

    Article  PubMed  CAS  Google Scholar 

  • Banuett F (1995) Genetics of Ustilago maydis, a fungal pathogen that induces tumors in maize. Annu Rev Genet 29:179–208

    Article  PubMed  CAS  Google Scholar 

  • Basehoar AD, Zanton SJ, Pugh BF (2004) Identification and distinct regulation of yeast tata box-containing genes. Cell 116:699–709

    Article  PubMed  CAS  Google Scholar 

  • Bell SP, Kobayashi R, Stillman B (1993) Yeast origin recognition complex functions in transcription silencing and DNA replication. Science (New York, NY) 262(5141):1844–1849

    Article  CAS  Google Scholar 

  • Borevitz JO, Ecker JR (2004) Plant genomics: the third wave. Annu Rev Genomics Hum Genet 5:443–477

    Article  PubMed  CAS  Google Scholar 

  • Burge CB, Karlin S (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8(3):346–354

    Article  PubMed  CAS  Google Scholar 

  • Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya A, Shibata K, Sasaki M, Izawa M, Muramatsu M, Hayashizaki Y, Schneider C (1996) High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37:327–336

    Article  PubMed  CAS  Google Scholar 

  • Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP (2010) Genome-wide functional analysis of human 5′ untranslated region introns. Genome Biol 11(3):R29

    PubMed  Google Scholar 

  • Chung BY, Simons C, Firth AE, Brown CM, Hellens RP (2006) Effect of 5′UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics 7:120

    Article  PubMed  Google Scholar 

  • Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190

    Article  PubMed  CAS  Google Scholar 

  • David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA 103(14):5320–5325

    Article  PubMed  CAS  Google Scholar 

  • Dobson MJ, Tuite MF, Roberts NA, Kingsman AJ, Kingsman SM, Perkins RE, Conroy SC, Fothergill LA (1982) Conservation of high efficiency promoter sequences in Saccharomyces cerevisiae. Nucleic Acids Res 10(8):2625–2637

    Article  PubMed  CAS  Google Scholar 

  • Gomez SM, Eiglmeier K, Segurens B, Dehoux P, Couloux A, Scarpelli C, Wincker P, Weissenbach J, Brey PT, Roth CW (2005) Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones. Genome Biol 6(4):R39

    Article  PubMed  Google Scholar 

  • Graber JH (2003) Variations in yeast 3′-processing cis-elements correlate with transcript stability. Trends Genet TIG 19(9):473–476

    Article  CAS  Google Scholar 

  • Graber JH, Cantor CR, Mohr SC, Smith TF (1999a) Genomic detection of new yeast pre-mRNA 3′-end-processing signals. Nucleic Acids Res 27(3):888–894

    Article  PubMed  CAS  Google Scholar 

  • Graber JH, Cantor CR, Mohr SC, Smith TF (1999b) In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc Natl Acad Sci USA 96(24):14055–14060

    Article  PubMed  CAS  Google Scholar 

  • Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 3(6):research0029.0021–0029.0012

    Google Scholar 

  • Hayashizaki Y (2003) The Riken mouse genome encyclopedia project. Comptes Rendus Biol 326(10–11):923–929

    Article  CAS  Google Scholar 

  • Ho EC, Cahill MJ, Saville BJ (2007) Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison. BMC Genomics [computer file] 8(1):334

    Article  Google Scholar 

  • Hogg JR, Goff SP (2010) Upf1 senses 3′UTR length to potentiate mRNA decay. Cell 143(3):379–389

    Article  PubMed  CAS  Google Scholar 

  • Hu J, Lutz CS, Wilusz J, Tian B (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA (New York, NY) 11(10):1485–1493

    CAS  Google Scholar 

  • Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296(5):1205–1214

    Article  PubMed  CAS  Google Scholar 

  • Hurowitz EH, Brown PO (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5(1):R2

    Article  PubMed  Google Scholar 

  • Kahmann R, Kämper J (2004) Ustilago maydis: how its biology relates to pathogenic development. New Phytol 164:31–42

    Article  CAS  Google Scholar 

  • Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, Wösten HA, de Vries R, Ruiz-Herrera J, Reynaga-Peña CG, Snetselaar K, McCann M, Pérez-Martín J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vraneš M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho EC, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J, Birren BW (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115):97–101

    Article  PubMed  Google Scholar 

  • Kuersten S, Goodwin EB (2003) The power of the 3′ UTR: translational control and development. Nat Rev Genet 4(8):626–637

    Article  PubMed  CAS  Google Scholar 

  • Laurie JD, Linning R, Bakkeren G (2008) Hallmarks of RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago maydis. Curr Genet 53(1):49–58

    Article  PubMed  CAS  Google Scholar 

  • Mandel CR, Bai Y, Tong L (2008) Protein factors in pre-mRNA 3′-end processing. Cell Mol Life Sci CMLS 65(7–8):1099–1122

    Article  CAS  Google Scholar 

  • Manley JL, Proudfoot NJ (1994) RNA 3′ ends: formation and function—meeting review. Genes Dev 8:259–264

    Article  PubMed  CAS  Google Scholar 

  • Mathé C, Sagot MF, Schiex T, Rouzé P (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 30(19):4103–4117

    Article  PubMed  Google Scholar 

  • Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T (2008) MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res 36(database issue): D196–D201

    Google Scholar 

  • Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci USA 103(47):17846–17851

    Article  PubMed  CAS  Google Scholar 

  • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (New York, NY) 320(5881):1344–1349

    Article  CAS  Google Scholar 

  • Neveu B, Belzile F, Belanger RR (2007) Cloning of the glyceraldehyde-3-phosphate dehydrogenase gene from Pseudozyma flocculosa and functionality of its promoter in two Pseudozyma species. Antonie van Leeuwenhoek 92(2):245–255

    Article  PubMed  CAS  Google Scholar 

  • Newlon CS (1988) Yeast chromosome replication and segregation. Microbiol Rev 52(4):568–601

    PubMed  CAS  Google Scholar 

  • 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):349–360

    Article  PubMed  CAS  Google Scholar 

  • Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y (2004) Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet Syst 79(4):227–232

    Article  PubMed  Google Scholar 

  • Pavy N, Rombauts S, Déhais P, Mathé C, Ramana DV, Leroy P, Rouzé P (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics (Oxford, England) 15(11):887–899

    Article  CAS  Google Scholar 

  • Ringnér M, Krogh M (2005) Folding free energies of 5′-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput Biol 1(7):e72

    Article  PubMed  Google Scholar 

  • Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16(10):939–945

    Article  PubMed  CAS  Google Scholar 

  • Rothnie HM, Reid J, Hohn T (1994) The contribution of AAUAAA and the upstream element UUUGUA to the efficiency of mRNA 3′-end formation in plants. EMBO J 13(9):2200–2210

    PubMed  CAS  Google Scholar 

  • Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, Mewes HW (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32(18):5539–5545

    Article  PubMed  CAS  Google Scholar 

  • Russo P, Li WZ, Hampsey DM, Zaret KS, Sherman F (1991) Distinct cis-acting signals enhance 3′ endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisiae. EMBO J 10(3):563–571

    PubMed  CAS  Google Scholar 

  • Sacadura NT, Saville BJ (2003) Gene expression and EST analyses of Ustilago maydis germinating teliospores. Fungal Genet Biol 40(1):47–64

    Article  PubMed  CAS  Google Scholar 

  • Sasaki T, Gilbert DM (2007) The many faces of the origin recognition complex. Curr Opin Cell Biol 19(3):337–343

    Article  PubMed  CAS  Google Scholar 

  • Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18(20):6097–6100

    Article  PubMed  CAS  Google Scholar 

  • Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science (New York, NY) 296(5565):141–145

    Article  Google Scholar 

  • Snetselaar KM, Mims CW (1992) Sporidial fusion and infection of maize seedlings by the smut fungus Ustilago maydis. Mycologia 84:193–203

    Article  Google Scholar 

  • Stein L (2001) Genome annotation: from sequence to biology. Nat Rev Genet 2(7):493–503

    Article  PubMed  CAS  Google Scholar 

  • Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formating protein and DNA sequences. Biotechniques 28:1102–1104

    PubMed  CAS  Google Scholar 

  • Tuller T, Ruppin E, Kupiec M (2009) Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics 10:391

    Article  PubMed  Google Scholar 

  • Venkataraman K, Brown KM, Gilmartin GM (2005) Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev 19(11):1315–1327

    Article  PubMed  CAS  Google Scholar 

  • Vilela C, McCarthy JE (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 5′ untranslated region. Mol Microbiol 49:859–867

    Article  PubMed  CAS  Google Scholar 

  • Wahle E (1995) 3′-end cleavage and polyadenylation of mRNA precursors. Biochim Biophys Acta 1261(2):183–194

    PubMed  Google Scholar 

  • Wahle E, Rüegsegger U (1999) 3′-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev 23(3):277–295

    PubMed  CAS  Google Scholar 

  • Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38(15):5075–5087

    Article  PubMed  CAS  Google Scholar 

  • Wang J, Holden DW, Leong SA (1988). Gene transfer system for the phytopathogenic fungus Ustilago maydis. Proc Natl Acad Sci USA 85(3):865–869

    Google Scholar 

  • Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453(7199):1239–1243

    Article  PubMed  CAS  Google Scholar 

  • Win J, Kanneganti TD, Torto-Alalibo T, Kamoun S (2006) Computational and comparative analyses of 150 full-length cDNA sequences from the oomycete plant pathogen Phytophthora infestans. Fungal Genet Biol 43(1):20–33

    Article  PubMed  CAS  Google Scholar 

  • Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A (2010) Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 11(8):R87

    Article  PubMed  Google Scholar 

  • Zhang L, Kasif S, Cantor CR, Broude NE (2004) GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci USA 101(48):16855–16860

    Article  PubMed  CAS  Google Scholar 

  • Zhao J, Hyman L, Moore C (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev MMBR 63(2):405–445

    CAS  Google Scholar 

  • Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD (2001) Reverse transcriptase template switching, a SMART approach for full-length cDNA library construction. Biotechniques 30:892–897

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We acknowledge the Natural Sciences and Engineering Research Council (NSERC) of Canada for funding BJS research grants. We acknowledge the Ontario Graduate Scholarship program and NSERC for fellowships for MED and CED. We would like to thank Natalie Gabovic for technical assistance.

Author information

Authors and Affiliations

  1. Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, K9J 7B8, Canada

    Colleen E. Doyle, Michael E. Donaldson, Erin N. Morrison & Barry J. Saville

  2. Forensic Science Program, Trent University, Peterborough, ON, K9J 7B8, Canada

    Barry J. Saville

Authors
  1. Colleen E. Doyle
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael E. Donaldson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Erin N. Morrison
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Barry J. Saville
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Barry J. Saville.

Additional information

Communicated by R. Fischer.

Electronic supplementary material

Below is the link to the electronic supplementary material.

438_2011_634_MOESM1_ESM.pdf

Online Resource 1 Identity and characteristics of full-length cDNAs. The column ‘Sequence Coverage’ indicates whether each FLcDNA contains the sequence of the 5’UTR, and/ or the 3’UTR. The lengths are reported for each UTR sequence. The column ‘Poly(A) Sites’ indicates the total number of different poly(A) addition sites identified for each FLcDNA (PDF 2117 kb)

Online Resource 2 Number of MUMDB genes represented in each dataset (PDF 342 kb)

Online Resource 3 Detailed summary of MUMDB genes not supported by new ESTs (PDF 242 kb)

438_2011_634_MOESM4_ESM.pdf

Online Resource 4 Length Distribution of 5’ and 3’UTRs. This bar graph presents the length distribution of a) the 5’UTRs and b) the 3’UTRs. The x-axis indicates the range of positions each bar covers (bin size = 50 bp) (PDF 364 kb)

438_2011_634_MOESM5_ESM.pdf

Online Resource 5 Distribution of 5’UTR and 3’UTR lengths relative to the median for each functional category: a) 5’UTR distribution. a) 3’UTR distribution (PDF 202 kb)

438_2011_634_MOESM6_ESM.pdf

Online Resource 6 A bar graph comparing the functional category distribution of the 94 genes with 5’UTR introns (PDF 199 kb)

438_2011_634_MOESM7_ESM.pdf

Online Resource 7 IPD motif characteristics. In this table, IPD motifs are presented as their WebLogo consensus motifs. The column ‘# of Sequences’ indicates the number of sequences in the IPD that have at least one occurrence of the motif. The column ‘# of Occurrences’ indicates the total number of times the motif occurs in all sequences. The median position is given in relation to the transcriptional start site (PDF 260 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Doyle, C.E., Donaldson, M.E., Morrison, E.N. et al. Ustilago maydis transcript features identified through full-length cDNA analysis. Mol Genet Genomics 286, 143–159 (2011). https://doi.org/10.1007/s00438-011-0634-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-011-0634-z

Keywords

Search

Navigation