Skip to main content

En/Spm-like transposons in Poaceae species: Transposase sequence variability and chromosomal distribution


Belonging to Class II of transposable elements, En/Spm transposons are widespread in a variety of distantly related plant species. Here, we report on the sequence conservation of the transposase region from sequence analyses of En/Spm-like transposons from Poaceae species, namely Zingeria biebersteiniana, Zingeria trichopoda, Triticum monococcum, Triticum urartu, Hordeum spontaneum, and Aegilops speltoides. The transposase region of En/Spm-like transposons was cloned, sequenced, and compared with equivalent regions of Oryza and Arabidopsis from the gene bank database. Southern blot analysis indicated that the En/Spm transposon was present in low (Hordeum spontaneum, Triticum monococcum, Triticum urartu) through medium (Zingeria bieberstiana, Zingeria trichopoda) to relatively high (Aegilops speltoides) copy numbers in Poaceae species. A cytogenetic analysis of the chromosomal distribution of En/Spm transposons revealed the concurence of the chromosomal localization of the En/Spm clusters with mobile clusters of rDNA. An analysis of En/Spm-like transposase amino acid sequences was carried out to investigate sequence divergence between 5 genera — Triticum, Aegilops, Zingeria, Oryza and Arabidopsis. A distance matrix was generated; apparently, En/Spm-like transposase sequences shared the highest sequence homology intra-generically and, as expected, these sequences were significantly diverged from those of O. sativa and A. thaliana. A sequence comparison of En/Spm-like transposase coding regions defined that the intra-genomic complex of En/Spm-like transposons could be viewed as relatively independent, vertically transmitted, and permanently active systems inside higher plant genomes.

The sequence data from this article was deposited in the EMBL/GenBank Data Libraries under the accession nos. AY707995-AY707996-AY707997-AY707998-AY707999-AY708000-AY708001-AY708002-AY708003-AY708004-AY708005-AY708005-AY265312.



transposable elements


terminal inverted repeats




  1. 1.

    Kumar, A. and Bennetzen, J.L. Plant retrotransposons. Annu. Rev. Genet. 33 (1999) 479–532.

    PubMed  CAS  Article  Google Scholar 

  2. 2.

    Danilevskaya, O., Slot, F., Pavlova, M. and Pardue, M.L. Structure of the Drosophila HeT-A transposon: a retrotransposon-like element forming telomeres. Chromosoma 103 (1994) 215–224.

    PubMed  CAS  Google Scholar 

  3. 3.

    Gray, Y.H. It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements. Trends Genet. 16 (2000) 461–468.

    PubMed  CAS  Article  Google Scholar 

  4. 4.

    Kidwell, M.G. and Holyoake, A.J. Transposon-Induced Hotspots for Genomic Instability. Genome Res. 11 (2001) 1321–1322.

    PubMed  CAS  Article  Google Scholar 

  5. 5.

    Xiong, Y. and Eickbush, T.H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9 (1990) 3353–3362.

    PubMed  CAS  Google Scholar 

  6. 6.

    Doolittle, R.F., Feng, D.F., Johnson, M.S. and Mclure, M.A. Origins and evolutionary relationships of retrovirus. Quarterly Rev. Biol. 64 (1989) 1–30.

    CAS  Article  Google Scholar 

  7. 7.

    Kunze, R., Saedler, H. and Lonnig, W. Plant transposable elements. Adv. Bot. Res. 27 (1997) 332–470.

    Google Scholar 

  8. 8.

    Staginnus, C.B., Huettel, C.D., Schmidt, T. and Kahl, G. A PCR-based assay to detect En/Spm-like transposon sequences in plants. Chromosome Res. 9 (2001) 591–605.

    PubMed  CAS  Article  Google Scholar 

  9. 9.

    Rhodes, P. and Vodkin, L. Organization of the Tgm family of transposable elements in soybean. Genetics 120 (1988) 597–604.

    PubMed  CAS  Google Scholar 

  10. 10.

    Shirsat, A. A transposon-like structure in the 5′ flanking sequence of the legumin gene from Pisum sativum. Mol. Genet. Genom. 212 (1988) 129–133.

    CAS  Article  Google Scholar 

  11. 11.

    Nacken, W., Pietrowiak, R., Saedler, H. and Sommer, H. The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specifity of insertion. Mol. Genet. Genom. 228 (1991) 201–208.

    CAS  Google Scholar 

  12. 12.

    Gierl, A. The En/Spm transposable element of maize. Curr. Topics Microbiol. Immunol. 204 (1996) 145–159.

    CAS  Google Scholar 

  13. 13.

    Snowden, K. and Napoli, C. PsI: a novel Spm-like transposable element from Petunia hybrida. Plant J. 14 (1998) 43–54.

    PubMed  CAS  Article  Google Scholar 

  14. 14.

    Aarts, M.G., Corzaan, P., Stiekema, W.J. and Pereira, A. A two-element Enhancer-Inhibitor transposon system in Arabidopsis thaliana. Mol. Gen. Genet 247 (1995) 555–564.

    PubMed  CAS  Article  Google Scholar 

  15. 15.

    Wisman, E., Hartmann, U., Sagasser, M., Baumann, E., Palme, K., Hahlbrock, K., Saedler, H. and Weisshaar, B. Knock-out mutants from an En-1 mutagenized Arabidopsis thaliana population generate phenylpropanoid biosynthesis phenotypes. Proc. Natl. Acad. Sci. USA 95 (1998) 12432–12437.

    PubMed  CAS  Article  Google Scholar 

  16. 16.

    Speulman, E., Metz, P.L.J., van Arkel, G., te Lintel Hekkert, B., Stiekma, W.J. and Pereira, A. A two-component Enhancer-Inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome. Plant Cell 11 (1999) 1853–1866.

    PubMed  CAS  Article  Google Scholar 

  17. 17.

    Tissier, A.F., Marillonnet, S., Klimyuk, V., Patel, K., Angel Torres, M., Murphy, G. and Jones, J.D.G. Multiple Independent Defective Suppressormutator Transposon Insertions in Arabidopsis: A Tool for Functional Genomics. Plant Cell 11 (1999) 1841–1852.

    PubMed  CAS  Article  Google Scholar 

  18. 18.

    Martinez, N.M., Greco, R., Van Arkel, G., Herrera-Estrella, L. And poson System in Arabidopsis. Plant Physiol. 129 (2002) 1544–1556.

    Article  Google Scholar 

  19. 19.

    Greco, R., Ouwerkerk, P.B.F., Taal, A.J.C., Sallaud, C., Guiderdoni, E., Meijer, A.H., Hoge, J.H.C. and Pereira., A. Transcription and somatic transposition of the maize En/Spm transposon system in rice. Mol. Gen. Genomics 270 (2004) 514–523.

    CAS  Article  Google Scholar 

  20. 20.

    Fedoroff, N.V. The Suppressor-mutator element and the evolutionary riddle of transposons. Genes Cells 4 (1999) 11–19.

    PubMed  CAS  Article  Google Scholar 

  21. 21.

    Kidwell, K.K. and Osborn, T.C. Simple plant DNA isolation procedures. In: Plant Genomes: Methods for genetic and physical mapping. (Beckmann J.S. and Osborn T.C., Eds.), Kluwer Academic Publishers, 1992, 1–13.

  22. 22.

    Raskina, O., Belyayev, A. and Nevo, E. Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch. Chromosome Res. 12 (2004a) 153–161.

    PubMed  CAS  Article  Google Scholar 

  23. 23.

    Altschul, S.F., Thomas, L.M., Alejandro, A.S., Jinghui, Z., Zheng, Z., Webb, M. and David, J.L. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389–3402.

    PubMed  CAS  Article  Google Scholar 

  24. 24.

    Pijnacker L.P. and Ferwerda, M.A. Giemsa C-banding of potato chromosomes. Can. J. Genet. Cytol. 26 (1984) 415–419.

    Google Scholar 

  25. 25.

    Belyayev, A., Raskina, O. and Nevo, E. Chromosomal distribution of reverse transcriptase containing retroelements in two Triticeae species. Chromosome Res. 9 (2001) 129–136.

    PubMed  CAS  Article  Google Scholar 

  26. 26.

    Taketa, S., Ando, H., Takeda, K., Harrison, G.E. and Heslop-Harrison, J.S. The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in genus Hordeum. Theor. Appl. Genet. 100 (2000) 169–176.

    CAS  Article  Google Scholar 

  27. 27.

    Raskina, O., Belyayev, A. and Nevo, E. Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA clusters variability in natural populations. Proc. Natl. Acad. Sci. USA 101 (2004b) 14818–14823.

    PubMed  CAS  Article  Google Scholar 

  28. 28.

    Aragon-Alcaide, L., Miller, T., Schwarzacher, T., Reader, S. and Moore, G. A cereal centromere sequence. Chromosoma 105 (1996) 261–268.

    PubMed  CAS  Article  Google Scholar 

  29. 29.

    Sumner, A.T. Chromosome banding and identification. in: Chromosome Analysis Protocols. (Gosden, J.R., Ed.), Methods in Molecular Biology. Humana Press Inc., Totowa, NJ, 29 (1994) 83–96.

    Google Scholar 

  30. 30.

    Giraldez, R., Cermeno, M.C. and Orellana, J. Comparison of C-banding pattern in chromosomes of inbred lines and open pollinated varieties of rye Secale cereale L. Z. Pflanzenzuecht 83 (1979) 40–48.

    Google Scholar 

  31. 31.

    Kubis, S.E., Castilho, A.M.M.F., Vershinin, A.V. and Heslop-Harrison, J.S. Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol. Biol. 52 (2003) 69–79.

    PubMed  CAS  Article  Google Scholar 

  32. 32.

    Saunders, V.A. and Houben, A. The pericentromeric heterochromatin of the grass Zingeria biebersteiniana (2n=4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences. Genome 44 (2001) 955–961.

    PubMed  CAS  Article  Google Scholar 

  33. 33.

    Pearce, S.R., Pich, U., Harrison, G., Flavell, A.J., Heslop-Harrison, J.S., Schubert, I. and Kumar, A. The Ty1-copia group retrotransposons, a major component of Allium cepa genome, are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 4 (1996) 357–364.

    PubMed  CAS  Article  Google Scholar 

  34. 34.

    Brandes, A., Heslop-Harrison, J.S., Kam, A., Kubis, S., Doudrick, R.L. and Schmidt, T. Comparative analysis of the chromosomal and genomic organization of Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol. Biol. 33 (1997) 11–21.

    PubMed  CAS  Article  Google Scholar 

  35. 35.

    Lippman, Z., Gendrel, A.V., Black, M., Vaughn, W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D., Carrington, J.C., Doerge, R.W., Colot, V. and Martienssen, R. The role of RNA interference in heterochromatic silencing. Nature 431 (2004) 364–370.

    PubMed  CAS  Article  Google Scholar 

  36. 36.

    Bennetzen, J. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42 (2000) 251–269.

    PubMed  CAS  Article  Google Scholar 

  37. 37.

    Zhang, J. and Peterson, T. Genome rearrangements by nonlinear transposons in maize. Genetics 153 (1999) 1403–1410.

    PubMed  CAS  Google Scholar 

  38. 38.

    Ellis, T.H.N., Poyser, S.J., Knox, M.R., Vershinin, A.V. and Ambrose, M.J. Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol. Genet. Gen. 260 (1998) 9–19.

    CAS  Google Scholar 

  39. 39.

    Fukuchi, A., Kikuchi, F. and Hirochika, H. DNA fingerprinting of cultivated rice with rice retrotransposon probes. Jpn. J. Genet. 68 (1993) 195–204.

    CAS  Article  Google Scholar 

  40. 40.

    Wolfe, K.H., Gouy, M., Yang, Y-W., Sharp, P.M. and Li, W-H. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86 (1989) 6201–6205.

    PubMed  CAS  Article  Google Scholar 

  41. 41.

    Jacobs, B.F., Kingston, J.D. and Jacobs, L.L. The origin of grass-dominated ecosystems. Ann. Mo. Bot. Gard. 86 (1999) 590–643.

    Article  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Ahu Altinkut.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Altinkut, A., Raskina, O., Nevo, E. et al. En/Spm-like transposons in Poaceae species: Transposase sequence variability and chromosomal distribution. Cell Mol Biol Lett 11, 214–229 (2006).

Download citation

Key words

  • Transposase
  • En/Spm
  • Poaceae
  • Sequence
  • Evolution
  • In situ hybridization