Functional & Integrative Genomics

, Volume 11, Issue 4, pp 671–677 | Cite as

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

  • Francis Parlange
  • Simone Oberhaensli
  • James Breen
  • Matthias Platzer
  • Stefan Taudien
  • Hana Šimková
  • Thomas Wicker
  • Jaroslav Doležel
  • Beat Keller
Short Communication

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.

Keywords

Blumeria graminis BAC library BAC-end sequences Transposable elements 

Abbreviations

Bg

Blumeria graminis

BES

BAC-end sequences

TE

Transposable element

Notes

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.

Supplementary material

10142_2011_240_MOESM1_ESM.doc (2 mb)
Supplementary Fig. 1Construction 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)
10142_2011_240_MOESM2_ESM.doc (24 kb)
Supplementary Fig. 2Insert 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)
10142_2011_240_MOESM3_ESM.doc (202 kb)
Supplementary Fig. 3BAC 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)
10142_2011_240_MOESM4_ESM.doc (92 kb)
Supplementary Fig. 4Size 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)
10142_2011_240_MOESM5_ESM.doc (126 kb)
Supplementary Fig. 5Distribution 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)
10142_2011_240_MOESM6_ESM.doc (31 kb)
Supplementary Table 1Overlapping 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)
10142_2011_240_MOESM7_ESM.doc (46 kb)
Supplementary Text(DOC 46 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Francis Parlange
    • 1
  • Simone Oberhaensli
    • 1
  • James Breen
    • 1
  • Matthias Platzer
    • 2
  • Stefan Taudien
    • 2
  • Hana Šimková
    • 3
  • Thomas Wicker
    • 1
  • Jaroslav Doležel
    • 3
  • Beat Keller
    • 1
  1. 1.Institute of Plant BiologyUniversity of ZurichZurichSwitzerland
  2. 2.Leibniz Institute for Age ResearchFritz Lipman InstituteJenaGermany
  3. 3.Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic

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