Abstract
We isolated and characterized different classes of transposable DNA elements in oil palm (Elaeis guineensis) plants grown from seed, and plants regenerated from tissue culture that show mantling, an abnormality leading to flower abortion. Using PCR assays, reverse transcriptase fragments belonging to LINE-like and gypsy-like retroelements and transposase fragments of En/Spm transposons were cloned. Sequence analysis revealed the presence of a major family of LINEs in oil palm, with other diverged copies. Gypsy-like retrotransposons form a single homologous group, whereas En/Spm transposons are present in several diverged families. Southern analysis revealed their presence in low (LINEs) to medium (gypsy and En/Spm) copy numbers in oil palm, and in situ hybridization showed a limited number of distinct loci for each class of transposable element. No differences in the genomic organization of the different classes of transposable DNA elements between ortet palm (parent) and regenerated palm trees with mantled phenotype were detected, but different levels of sequence methylation were observed. During tissue culture, McrBC digestion revealed the genome-wide reduction in DNA methylation, which was restored to near-normal levels in regenerated trees. HPLC analysis showed that methylation levels were slightly lower in the regenerated trees compared to the ortet parent. The genomic organization of the transposable DNA elements in different oil palm species, accessions and individual regenerated trees was investigated revealing only minor differences. The results suggest that the mantled phenotype is not caused by major rearrangements of transposable elements but may relate to changes in the methylation pattern of other genomic components.
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Altschul, S., Gish, W., Miller, W., Myers, E. and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.
Beguiristain, T., Grandbastien, M.A., Puigdomènech, P. and Casacuberta, J.M. 2001. Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol. 127: 212–221.
Bureau, T.E. and Wessler S.R. 1994. Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6: 907–916.
Castilho, A., Neves, N., Rufini-Castiglione, M., Viegas, W. and Heslop-Harrison, J.S. 1999. 5-Methylcytosine distribution and genome organization in Triticale before and after treatment with 5-azacytidine. J. Cell Sci. 112: 4397–4404.
Castilho, A., Vershinin, A. and Heslop-Harrison, J.S. 2000. Repetitive DNA and the chromosomes in the genome of oil palm (Elaeis guineensis). Ann. Bot. 85: 837–844.
Cubas, P., Vincent, C. and Coen, E. 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157–161.
Dombroski, B.A., Mathias, S.L., Nanthakumar, E., Scott, A.F. and Kazazian, H.H. Jr. 1991. Isolation of an active human transposable element. Science 254: 1805–1808.
Feinberg, A.P. and Vogelstein, B. 1983. A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Ann. Biochem. 137: 266–267.
Feschotte, C., Jiang, N. and Wessler, S.R. 2002. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3: 329–341.
Friesen, N., Brandes, A. and Heslop-Harrison, J.S. 2001. Diversity, origin and distribution of retrotransposons (gypsy and copia) in conifers. Mol. Biol. Evol. 18: 1176–1188.
Gindullis, F., Desel, C., Galasso, I. and Schmidt, T. 2001. The largescale organization of the centromeric region in Beta species. Genome Res. 11: 253–265.
Grandbastien, M.-A. 1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3: 181–187.
Hansen, L.J., Chalker, D.L. and Sandmeyer, S.B. 1988. Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses. Mol. Cell. Biol. 8: 5245–5256.
Higgins, D. and Sharp, P. 1988. CLUSTAL: a package for performing multiple sequence alignments on a microcomputer. Gene 73: 237–244.
Hirochika, H. 1993. Activation of tobacco retrotransposons during tissue culture. EMBO J. 12: 2521–2528.
Jacobsen, S.E. and Meyerowitz, E.M. 1997. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277: 1100–1103.
Jaligot, E., Rival, A., Beule, T., Dussert, S. and Verdeil, J.L. 2000. Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep. 19: 684–690.
Kaeppler, S.M., Kaeppler, H.F. and Rhee, Y. 2000. Epigenetic aspects of somaclonal variation in plants. Plant Mol. Biol. 43: 179–188.
Kubis, S., Heslop-Harrison, J.S. and Schmidt, T. 1997. A family of differentially amplified DNA sequences in the genus Beta reveals genetic variation in Beta vulgaris subspecies and cultivars. J. Mol. Evol. 44: 310–320.
Kubis, S., Schmidt, T. and Heslop-Harrison, J.S. 1998a. Repetitive DNA elements as a major component of plant genomes. Ann. Bot. 82S: 45–55.
Kubis, S.E., Heslop-Harrison, J.S., Desel, C. and Schmidt, T. 1998b. The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms. Plant Mol. Biol. 36: 821–831.
Kumekawa, N., Ohtsubo, E. and Ohtsubo, H. 1999. Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom. Genes Genet. Syst. 74: 299–307.
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.
Marlor, R.L., Parkhurst, S.M. and Corces, V.G. 1986. The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins. Mol. Cell Biol. 6: 1129–1134.
Miura, A., Yonebayashi, S., Watanabe, K., Toyama, T., Shimada, H. and Kakutani T. 2001. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212–214.
Nacken, W.K., Piotrowiak, R., Saedler, H. and Sommer, H. 1991. The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specificity of insertion. Mol. Gen. Genet. 228: 201–208.
Pereira, A., Cuypers, H., Gierl, A., Schwarz-Sommer, Z.S. and Saedler, H. 1986. Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J. 5: 835–841.
Price, Z., Dumortier, F., MacDonald, D.W. and Mayes, S. 2002. Characterization of copia-like retrotransposons in oil palm (Elaeis guineensis Jacq.) Theor. Appl. Genet. 104: 860–867.
Rival, A., Beule, T., Barre, P., Hamon, S., Duval, Y. and Noiret, M. 1997. Comparative flow cytometric estimation of nuclear DNA content in oil palm (Elaeis guineensis Jacq) tissue cultures and seed-derived plants. Plant Cell Rep. 16: 884–887.
Schwarz-Sommer, Z., Leclercq, L., Goebel, E. and Saedler, H. 1987. Cin4, an insert altering the structure of the A1 gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 13: 3873–3880.
Schwarzacher, T. and Heslop-Harrison, J.S. 2000. Practical In Situ Hybridization. Bios, Oxford, 203+xii pp.
Staginnus, C., Huettel, B., Desel, C., Schmidt, T. and Kahl, G. 2001. A PCR-based assay to detect En/Spm-like transposon sequences in plants. Chromosome Res. 9: 591–605.
Sutherland, E., Coe, L. and Raleigh, E.A. 1992. Mcrbc: a multisubunit gtp-dependent restriction endonuclease. J. Mol. Biol. 225: 327–348.
Vershinin, A.V., Druka, A., Alkhimova, A.G., Kleinhofs, A. and Heslop-Harrison, J.S. 2002. LINEs and gypsy-like retrotransposons in Hordeum species. Plant Mol. Biol. 49: 1–14.
Wendel, J.F. and Wessler, S.R. 2000. Retrotransposon-mediated genome evolution on a local ecological scale. Proc. Natl. Acad. Sci. USA 97: 6250–6252.
Wolffe, A.P. and Matzke, M.A. 1999. Epigenetics: Regulation through repression. Science 286: 481–486.
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.
Xiong, Y. and Eickbush, T.H. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353–3362.
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Kubis, S.E., Castilho, A.M., Vershinin, A.V. et al. Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol Biol 52, 69–79 (2003). https://doi.org/10.1023/A:1023942309092
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DOI: https://doi.org/10.1023/A:1023942309092