Plant Molecular Biology

, Volume 40, Issue 6, pp 903–910 | Cite as

LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes

  • Thomas Schmidt


Retroelements and remnants thereof constitute a large fraction of the repetitive DNA of plant genomes. They include LTR (long terminal repeat) retrotransposons such as Ty1-copia and Ty3-gypsy retrotransposons, which are widespread in plant genomes and show structural similarity to retroviruses. Recently, non-LTR retrotransposons, lacking the long terminal repeats and subdivided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements), have been discovered as ubiquitous components of nuclear genomes in many species across the plant kingdom. LINEs are probably the most ancient class of retrotransposons in plant genomes, but the evolutionary borders between non-LTR retrotransposons, LTR retrotransposons and retroviruses are indistinct as shown by the detection of intermediate forms in other eukaryotic taxa. Transposition of non-LTR retrotransposons is only rarely observed in plants indicating that the majority of these retroelements are inactive and/or under regulation of the host genome. Transposition is poorly understood, but experimental evidence from other genetic systems, in particular from insect and mammalian species, shows that LINEs are able to transpose autonomously, while non-autonomous SINEs depend on the reverse transcription machinery of other retrotransposons. Fluorescence in situ hybridization demonstrated that different classes of retrotransposons differ largely in their chromosomal organization and are often excluded from blocks of rapidly homogenizing tandem repeats. In particular, LINEs contribute considerably to the repetitive DNA of nuclear plant genomes.

non-LTR retrotransposons retroposon transposable elements LINE (long interspersed nuclear elements) SINE (short interspersed nuclear elements) reverse transcriptase 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bennetzen, J.L. and Kellogg, E.A. 1997. Do plants have a one-way ticket to genomic obesity? Plant Cell 9: 1509–1514.PubMedGoogle Scholar
  2. Boeke, J.D. 1997. LINEs and Alus: the polyA connection. Nature Genet.16: 6–7.Google Scholar
  3. Danilevskaya, O.N., Arkhipova, I.R., Traverse, K.L. and Pardue, M.L. 1997. Promoting in tandem: the promotor for telomere transposons Het-Aand implications for the evolution of retroviral LTRs. Cell 88: 647–655.PubMedGoogle Scholar
  4. Deragon, J.M., Gilbert, N., Rouquet, L., Lenoir, A., Arnaud, P. and Picard, G. 1996. A transcriptional analysis of the S1Bn (Brassica napus) family of SINE. Plant Mol. Biol. 32: 869–878.PubMedGoogle Scholar
  5. Eickbush, T.H. 1994. Origin and evolutionary relationships of retroelements. In: S.S. Morse (Ed.), The Evolutionary Biology of Viruses, Raven Press, New York, pp. 121–157.Google Scholar
  6. Eickbush, T.H. 1997. Telomerase and retrotransposons: which came first? Science 277: 911–912.PubMedGoogle Scholar
  7. Feng, Q., Moran, J.V., Kazazian, H.H. Jr. and Boeke, J.D. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for a retrotransposase required for retrotransposition. Cell 87: 905–916.PubMedGoogle Scholar
  8. Feng, Q., Schumann, G. and Boeke, J.D. 1988. Retrotransposon R1Bm endonuclease cleaves the target sequence. Proc. Natl. Acad. Sci. USA 95: 2083–2088.Google Scholar
  9. Finnegan, D.J. 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103–107.Google Scholar
  10. Flavell, A.J., Pearce, S.R. and Kumar, A. 1994. Plant transposable elements and the genome. Curr. Opin. Genet. Dev. 4: 838–844.PubMedGoogle Scholar
  11. Goubely, C., Arnaud, P., Tatout, C., Heslop-Harrison, J.S. and Deragon, J.M. 1999. S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in Brassica napus: identification of a preferred target site for asymmetrical methylation. Plant Mol. Biol. 39: 243–255.PubMedGoogle Scholar
  12. Grandbastien, M.A. 1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3: 181–187.CrossRefGoogle Scholar
  13. Higashiyama, T., Noutoshi, Y., Fujie, M. and Yamada, T. 1997. Zepp, a LINE-like retrotransposon accumulated in the Chlorellatelomeric region. EMBO J 16: 3715–3723.PubMedGoogle Scholar
  14. Knoop, V., Unseld, M., Marienfeld, J., Brandt, P., Sünkel, S., Ullrich, H. and Brennicke, A. 1996. copia-gypsy-and LINElike retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana. Genetics 142: 579–585.PubMedGoogle Scholar
  15. Kubis, S., Heslop-Harrison, J.S., Desel, C. and Schmidt, T. 1998. The genomic organization of non-LTR retrotransposons (LINEs) from three Betaspecies and five other angiosperms. Plant Mol. Biol. 36: 821–831.PubMedGoogle Scholar
  16. Kumar, A. 1998. The evolution of plant retroviruses: moving to green pastures. Trends Plant Sci. 3: 371–374.Google Scholar
  17. Kunze, R., Saedler, H. and Lönnig, W.E. 1997. Plant transposable elements. In: J.A. Callow (Ed.), Advances in Botanical Research, Vol. 27, Academic Press, San Diego/London etc., pp. 331–470.Google Scholar
  18. Leeton, P.R.J. and Smyth, D.R. 1993. An abundant LINE-like element amplified in the genome of Lilium speciosum. Mol. Gen. Genet. 237: 97–104.Google Scholar
  19. Lenoir, A., Cournoyer, B., Warwick, S., Picard, G. and Deragon, J.M. 1997. Evolution of SINE S1 retroposons in Cruciferae plant Species. Mol. Biol. Evol. 14: 934–941.PubMedGoogle Scholar
  20. Luan, D.D., Korman, M.H., Jakubczak, J.L. and Eickbush, T.H. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595–605.PubMedGoogle Scholar
  21. Mochizuki, K., Umeda, M., Ohtsubo, H. and Ohtsubo, 1992. Characterization of a plant SINE, pSINE1, in rice genomes. Jpn. J. Genet. 57: 155–166.Google Scholar
  22. Moran, J.V., DeBerardinis, R.J. and Kazazian, H.H. Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530–1534.PubMedGoogle Scholar
  23. Noma, K., Ohtsubo, E. and Ohtsubo, H. 1999. Non-LTR retrotransposons (LINEs) as ubiquitous components of plant genomes. Mol. Gen. Genet. 261: 71–79.PubMedGoogle Scholar
  24. Noutoshi, Y., Arai, R., Fujie, M. and Yamada, T. 1998. Structure of the Chlorella Zeppretrotransposon: Zeppclusters in the genome. Mol. Gen. Genet. 259: 256–263.PubMedGoogle Scholar
  25. Ohshima, K., Hamada, M., Terai, Y. and Okada, N. 1996. The 30-ends of tRNA-derived short interspersed repetitive elements are derived from the 30-ends of long interspersed repetitive elements. Mol. Cell. Biol. 16: 3756–3764.Google Scholar
  26. Pardue, M.L., Danilevskaya, O.N., Traverse, K.L. and Lowenhaupt, K. 1997. Evolutionary links between telomeres and transposable Elements. Genetica 100: 73–84.PubMedGoogle Scholar
  27. SanMiguel, P., Tikhonov, A., Jin, Y.-K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., Avramova, Z., and Bennetzen, J.L. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765–768.Google Scholar
  28. Schmidt, T. and Heslop-Harrison, J.S. 1998. Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci. 3: 195–199.Google Scholar
  29. Schmidt, T., Kubis, S. and Heslop-Harrison, J.S. 1995. Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgarisL.): LINEs and Ly1-copia-like elements as major components of the genome. Chrom. Res. 3: 335–345.PubMedGoogle Scholar
  30. Schwarz-Sommer, Z., Leclercq, L., Goebel, E. and Saedler, H. 1987. Cin4, an insert altering the structure of the A1gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 13: 3873–3880.Google Scholar
  31. Tatout, C., Lavie, L. and Deragon, J.M. 1998. Similar target site selection occurs in integration of plant and mammalian retroposons. J. Mol. Evol. 47: 463–470.PubMedGoogle Scholar
  32. Wessler, S.R., Bureau, T.E. and White, S.E. 1995. LTRretrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814–821.PubMedGoogle Scholar
  33. Wright, D.A., Ke, N., Smalle, J., Hauge, B.M., Goodman, H.M. and Voytas, D.F. 1996. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. Genetics 142: 569–578.PubMedGoogle Scholar
  34. Xiong, Y. and Eickbush, T.H. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J.9: 3353–3362.PubMedGoogle Scholar
  35. Yoshioka, Y., Matsumoto, S., Kojima, S., Ohshima, K., Okada, N. and Machida, Y. 1993. Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc. Natl. Acad. Sci. USA: 90: 6562–6566.PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 1999

Authors and Affiliations

  • Thomas Schmidt
    • 1
  1. 1.Plant Molecular Cytogenetics Group, Institute of Crop Science and Plant BreedingChristian Albrechts University of KielKielGermany

Personalised recommendations