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A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome

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Abstract

Powdery mildew of wheat (Triticum aestivum L.) is caused by the ascomycete fungus Blumeria graminis f.sp. tritici. Genomic approaches open new ways to study the biology of this obligate biotrophic pathogen. We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome using the 454 technology and the construction of the first genomic bacterial artificial chromosome (BAC) library for this fungus. High-coverage contigs were assembled with the 454 reads. They allowed the characterization of 56 transposable elements and the establishment of the Blumeria repeat database. The BAC library contains 12,288 clones with an average insert size of 115 kb, which represents a maximum of 7.5-fold genome coverage. Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. This explains the unusually large size of this genome which we estimate to be at least 174 Mb, based on a large-scale physical map constructed through the fingerprinting of the BAC library. Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence.

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Abbreviations

Bg :

Blumeria graminis

BES:

BAC-end sequences

TE:

Transposable element

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, Delehaunty K, Dong S, Downton P, Dumas B, Fabro G, Fronick C, Fuerstenberg SI, Fulton L, Gaulin E, Govers F, Hughes L, Humphray S, Jiang RH, Judelson H, Kamoun S, Kyung K, Meijer H, Minx P, Morris P, Nelson J, Phuntumart V, Qutob D, Rehmany A, Rougon-Cardoso A, Ryden P, Torto-Alalibo T, Studholme D, Wang Y, Win J, Wood J, Clifton SW, Rogers J, Van den Ackerveken G, Jones JD, McDowell JM, Beynon J, Tyler BM (2010) Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 330:1549–1551

    Article  PubMed  CAS  Google Scholar 

  • Brunner S, Hurni S, Streckeisen P, Mayr G, Albrecht M, Yahiaoui N, Keller B (2010) Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles. Plant J 64:433–445

    Article  PubMed  CAS  Google Scholar 

  • Chang YL, Cho S, Kistler HC, Hsieh CS, Muehlbauer GJ (2007) Bacterial artificial chromosome-based physical map of Gibberella zeae (Fusarium graminearum). Genome 50:954–962

    Article  PubMed  CAS  Google Scholar 

  • Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr MG, Kodira CD, Kohler A, Kües U, Lindquist EA, Lucas SM, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tanguay P, Tuskan GA, Henrissat B, Van de Peer Y, Rouzé P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci USA 108:9166–9171

    Article  PubMed  CAS  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred I Accuracy assessment. Genome Res 8:175–185

    PubMed  CAS  Google Scholar 

  • Glawe DA (2008) The powdery mildews: a review of the world’s most familiar (yet poorly known) plant pathogens. Annu Rev Phytopathol 46:27–51

    Article  PubMed  CAS  Google Scholar 

  • Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD (2007) Eukaryotic genome size databases. Nucleic Acids Res 35:D332–D338

    Article  PubMed  CAS  Google Scholar 

  • Inuma T, Khodaparast SA, Takamatsu S (2007) Multilocus phylogenetic analyses within Blumeria graminis, a powdery mildew fungus of cereals. Mol Phylogenet Evol 44:741–751

    Article  PubMed  CAS  Google Scholar 

  • Martin F, Aerts A, Ahren D, Brun A, Danchin EGJ, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buee M, Brokstein P, Canback B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbe J, Lin YC, Legue V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Kues U, Lucas S, Van de Peer Y, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouze P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92

    Article  PubMed  CAS  Google Scholar 

  • Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buee M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marcais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, Wincker P (2010) Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464:1033–1038

    Article  PubMed  CAS  Google Scholar 

  • Nowrousian M, Stajich JE, Chu ML, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Poggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kuck U, Freitag M (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 6:e1000891

    Article  PubMed  Google Scholar 

  • Oberhaensli S, Parlange F, Buchmann JP, Jenny FH, Abbott JC, Burgis TA, Spanu PD, Keller B, Wicker T (2011) Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution. Fungal Genet Biol. doi:101016/jfgb201010003

  • Pedersen C, Wu B, Giese H (2002) A Blumeria graminis f.sp. hordei BAC library—contig building and microsynteny studies. Curr Genet 42:103–113

    Article  PubMed  CAS  Google Scholar 

  • Rasmussen M, Rossen L, Giese H (1993) SINE-like properties of a highly repetitive element in the genome of the obligate parasitic fungus Erysiphe graminis f.sp. hordei. Mol Gen Genet 239:298–303

    PubMed  CAS  Google Scholar 

  • Ridout CJ, Brown JKM (1999) Physical mapping of avirulence genes in the barley powdery mildew pathogen Erysiphe graminis f.sp. hordei (abstract). The First International Powdery Mildew Conference, Palais des Papes, Avignon, France, 29 August–2 September

  • Scalabrin S, Morgante M, Policriti A (2009) Automated fingerprint background removal: FPB. BMC Bioinforma 10:127

    Article  Google Scholar 

  • Soderlund C, Longden I, Mott R (1997) FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci 13:523–535

    PubMed  CAS  Google Scholar 

  • Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167:GC1-10

    Google Scholar 

  • Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stüber K, Loren V, van Themaat E, Brown JKM, Butcher SA, Gurr SJ, Lebrun M-H, Ridout CJ, Schulze-Lefert P, Talbot NJ, Ahmadinejad N, Ametz C, Barton GR, Benjdia M, Bidzinski P, Bindschedler LV, Both M, Brewer MT, Cadle-Davidson L, Cadle-Davidson MM, Collemare J, Cramer R, Lopez-Ruiz F, Frenkel O, Godfrey D, Harriman J, Hoede C, King BC, Klages S, Kleemann J, Knoll D, Koti PS, Kreplak J, Lu X, Maekawa T, Mahanil S, Milgroom MG, Montana G, Noir S, O’Connell RJ, Oberhaensli S, Parlange F, Pedersen C, Quesneville H, Reinhardt R, Rott M, Sacristán S, Schmidt SM, Schön M, Skamnioti P, Sommer H, Stephens A, Takahara H, Thordal-Christensen H, Vigouroux M, Weßling R, Wicker T, Panstruga R (2010) Genome expansion and gene loss in powdery mildew fungi reveal functional tradeoffs in extreme parasitism. Science 330:1543–1546

    Article  PubMed  CAS  Google Scholar 

  • Stojiljkovic I, Bozja J, Salajsmic E (1994) Molecular-cloning of bacterial-DNA in-vivo using a transposable R6k ori and a P1vir phage. J Bacteriol 176:1188–1191

    PubMed  CAS  Google Scholar 

  • Wei YD, Collinge DB, SmedegaardPetersen V, ThordalChristensen H (1996) Characterization of the transcript of a new class of retroposon-type repetitive element cloned from the powdery mildew fungus, Erysiphe graminis. Mol Gen Genet 250:477–482

    PubMed  CAS  Google Scholar 

  • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  PubMed  CAS  Google Scholar 

  • You FM, Luo MC, Gu YQ, Lazo GR, Deal K, Dvorak J, Anderson OD (2007) GenoProfiler: batch processing of high-throughput capillary fingerprinting data. Bioinformatics 23:240–242

    Article  PubMed  CAS  Google Scholar 

  • Zhang X, Scheuring C, Tripathy S, Xu Z, Wu C, Ko A, Tian SK, Arredondo F, Lee MK, Santos FA, Jiang RHY, Zhang HB, Tyler BM (2006) An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact 19:1302–1310

    Article  PubMed  CAS  Google Scholar 

  • Zhu H, Choi SD, Johnston AK, Wing RA, Dean RA (1997) A large-insert (130 kbp) bacterial artificial chromosome library of the rice blast fungus Magnaporthe grisea: genome analysis, contig assembly, and gene cloning. Fungal Genet Biol 21:337–347

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We would like to thank Gabriele Büsing for the excellent technical assistance. We thank the Blugen consortium (www.blugen.org) and especially Dr. P. Spanu for access to the barley powdery mildew genome sequences. This work was supported by the Swiss National Science Foundation grant 3100A-127061/1 (BK), an advanced grant of the European Research Council (durable resistance 249996, BK) and by European Union grant no. ED0007/01/01 Centre of the Region Haná for Biotechnological and Agricultural Research (HŠ, JD).

Ethical standards

The experiments presented in this study comply with the current laws of the country in which they were performed.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland

    Francis Parlange, Simone Oberhaensli, James Breen, Thomas Wicker & Beat Keller

  2. Leibniz Institute for Age Research, Fritz Lipman Institute, Beutenbergstrasse 11, 007745, Jena, Germany

    Matthias Platzer & Stefan Taudien

  3. Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 77200, Olomouc, Czech Republic

    Hana Šimková & Jaroslav Doležel

Authors
  1. Francis Parlange
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  2. Simone Oberhaensli
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  3. James Breen
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  4. Matthias Platzer
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  5. Stefan Taudien
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  6. Hana Šimková
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  7. Thomas Wicker
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  8. Jaroslav Doležel
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  9. Beat Keller
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Corresponding author

Correspondence to Beat Keller.

Additional information

Francis Parlange and Simone Oberhaensli contributed equally to this work

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Supplementary Fig. 1

Construction of a BAC library from Bg tritici DNA. a Digestibility tests of HMW DNA. DNA was tested for digestibility using restriction enzyme HindIII. Lane 1: undigested control; lane 2: partial digestion with 10 U/ml for 20 min; lane 3: complete digestion with 100 U/ml for 6 h; lane 4: 1-kb ladder; lane 5: MidRange PFG Marker I. b Insert size analysis of 27 randomly selected BAC clones. BAC DNA was digested with NotI and separated by PFGE. Markers on the left are the Lambda Ladder PFG Marker and MidRange Marker I (DOC 2039 kb)

Supplementary Fig. 2

Insert size distribution in the BAC library. Insert sizes were analyzed in 300 BAC clones randomly selected from the three fractions of the library (B, M1, M2). The overall distribution of insert sizes was calculated by combining data from the three fractions considering their proportion in the library (DOC 24 kb)

Supplementary Fig. 3

BAC contigs comprising locus 2 and locus GTCA_E4. a Contig ctg5, harboring the locus 2 (Oberhaensli et al. 2011). b Contig ctg25, harboring the locus GTCA_E4. Scale is in kilobases. BAC clones identified by PCR screening of the library are highlighted in gray. Red boxes at the BAC ends indicate the availability of the respective BES (note that the orientation is unknown). The graphical representation was produced based on the FPC files and using WICKERsoft software (DOC 202 kb)

Supplementary Fig. 4

Size distribution of BAC-end sequence (BES) length. A total of 20,001 BES were generated by the sequencing from both ends of the entire BAC library. The average read length is 633 bp with 82% of the reads being above 500 bp. The peak observed at 263 bp is caused by 54 identical sequences which were shown by BLAST analyses to correspond to the sequence of the origin of replication “transposable R6K ori” (Stojiljkovic et al. 1994) (DOC 91 kb)

Supplementary Fig. 5

Distribution of the ten most abundant TE families of the Blumeria repeat database in the BES. Bgt and Bgh indicate origin of TE (Bg tritici and Bg hordei, respectively). Names are according to the nomenclature of Wicker et al. (2007): RSX, SINE (pink); RIX, LINE (green); RLG, Gypsy (yellow); XXX, unclassified (blue). (DOC 126 kb)

Supplementary Table 1

Overlapping BAC clones for two genomic regions. PCR screening of the library was done on plates 1 to 16. Molecular markers used to screen for locus 2 have been described in Oberhaensli et al. (2011). Screening for locus GTCA_E4 was done with molecular marker GTCA_E4 (Parlange and Keller, unpublished data) (DOC 31 kb)

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Parlange, F., Oberhaensli, S., Breen, J. et al. A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome. Funct Integr Genomics 11, 671–677 (2011). https://doi.org/10.1007/s10142-011-0240-5

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