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Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome

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Abstract

The barley BARE-1 is a transcribed, copia-like retroelement with well-conserved functional domains, an active promoter, and a copy number of at least 3 × 104. We examined its chromosomal localization by in situ hybridization. The long terminal repeat (LTR) probe displayed a uniform hybridization pattern over the whole of all chromosomes, excepting paracentromeric regions, telomeres, and nucleolar organizer (NOR) regions. The integrase probe showed a similar pattern. The 5′-untranslated leader (UTL) probe, expected to be the most rapidly evolving component, labeled chromosomes in a dispersed and non-uniform manner, concentrated in the distal regions, possibly indicating a targe site preference.

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References

  1. Abbo S, Dunford RP, Foote TN, Reader SM, Flavell RB, Moore G: Organization of retro-element and stem-loop repeat families in the genomes and nuclei of cereals. Chromosome Res 3: 5–15 (1995).

    PubMed  Google Scholar 

  2. Ahn S, Anderson JA, Sorrells ME, Tanksley SD: Homeologous relationships of rice, wheat, and maize chromosomes. Mol Gen Genet 241: 483–490 (1993).

    PubMed  Google Scholar 

  3. Ahn S, Tanksley SD: Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980–7984 (1993).

    PubMed  Google Scholar 

  4. Anamthawat-Jónsson K, Reader SM: Pre-annealing of total genomic DNA probes for simultaneous in situ hybridization in cereal species. Genome 38: 814–816 (1995).

    PubMed  Google Scholar 

  5. Boeke JD, Corces VG: Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol 43: 403–434 (1989).

    Article  PubMed  Google Scholar 

  6. Bureau TE, Wessler SR: Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4: 1283–1294 (1992).

    Article  PubMed  Google Scholar 

  7. Bureau TE, Wessler SR: Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc Natl Acad Sci USA 91: 1411–1415 (1994).

    PubMed  Google Scholar 

  8. Bureau TE, Wessler SR: Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6: 907–916 (1994).

    Article  PubMed  Google Scholar 

  9. Chalker DL, Sandmeyer SB: Transfer RNA genes are genomic targets for de novo transposition of the yeast retrotransposon Ty3. Genetics 126: 837–850 (1990).

    PubMed  Google Scholar 

  10. Doolittle RF, Feng D-F, Johnson MS, McClure MA: Origins and evolutionary relationships of retroviruses. Q Rev Biol 64: 1–30 (1989).

    Article  PubMed  Google Scholar 

  11. Finnegan DJ: Eukaryotic transposable elements and genome evolution. Trends Genet 5: 103–107 (1989).

    Article  PubMed  Google Scholar 

  12. Flavell AJ, Smith DR, Kumar A: Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 231: 233–242 (1992).

    PubMed  Google Scholar 

  13. Flavell RB, O'Dell M, Hutchinson J: Nucleotide sequence organization in plant chromosomes and evidence for sequence translocation during evolution. Cold Spring Harbor Symp Quant Biol 45: 501–508 (1981).

    PubMed  Google Scholar 

  14. Grandbastien M-A: Retroelements in higher plants. Trends Genet 8: 103–108 (1992).

    PubMed  Google Scholar 

  15. Grandbastien M-A, Spielmann A, Caboche M: Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376–380 (1989).

    PubMed  Google Scholar 

  16. Hajihosseini M, Iavachev L, Price J: Evidence that retroviruses integrate into post-replication host DNA. EMBO J 12: 4969–4974 (1993).

    PubMed  Google Scholar 

  17. Hirochika H, Fukuchi A, Kikuchi F: Retrotransposon families in rice. Mol Gen Genet 233: 209–216 (1992).

    PubMed  Google Scholar 

  18. Ji H, Moore DP, Blomberg MA, Braiterman LT, Voytas DF, Natsoulis G, Boeke JD: Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73: 1007–1018 (1993).

    Article  PubMed  Google Scholar 

  19. Johns MA, Babcock MS, Fuerstenberg SM, Fuerstenberg SI, Freeling M, Simpson RB: An unusually compact retrotransposon in maize. Plant Mol Biol 12: 633–642 (1989).

    Google Scholar 

  20. Joshi CP, Nguyen HT: 5′ untranslated leader sequences of eukaryotic mRNAs encoding heat shock induced proteins. Nucl Acids Res 23: 541–549 (1995).

    PubMed  Google Scholar 

  21. Konieczny A, Voytas DF, Cummings MP, Ausubel FM: A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127: 801–809 (1991).

    PubMed  Google Scholar 

  22. Kozak M: Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem 266: 19867–19870 (1991).

    PubMed  Google Scholar 

  23. Lee D, Ellis THN, Turner L, Hellens RP, Cleary WG: A copia-like element in Pisum demonstrates the use of dispersed repeated sequences in genetic analysis. Plant Mol Biol 15: 707–722 (1990).

    Article  PubMed  Google Scholar 

  24. Manninen I, Schulman AH: BARE-1, a Copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol 22: 829–846 (1993).

    Article  PubMed  Google Scholar 

  25. Moore G, Cheung W, Schwarzacher T, Flavell R: BIS 1, a major component of the cereal genome and a tool for studying genomic organization. Genomics 19: 469–476 (1991).

    Google Scholar 

  26. Moore G, Lucas H, Batty N, Flavell R: A family of retrotransposons and associated genomic variation in wheat. Genomics 10: 461–468 (1991).

    PubMed  Google Scholar 

  27. Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ: The Ty1-copia group of retrotransposons in Vicia species: copy number sequence heterogeneity and chromosomal localisation. Mol Gen Genet, in press (1996).

  28. Pouteau S, Huttner E, Grandbastien M-A, Caboche M: Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J 10: 1911–1918 (1991).

    PubMed  Google Scholar 

  29. Pouteau S, Spielmann A, Meyer C, Grandbastien M-A, Caboche M: Effects of Tnt1 tobacco retrotransposon insertion on target gene transcription. Mol Gen Genet 228: 233–239 (1991).

    Article  PubMed  Google Scholar 

  30. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989).

    Google Scholar 

  31. Sandmeyer SB, Hansen LJ, Chalker DL: Integration specificity of retrotransposons and retroviruses. Annu Rev Genet 24: 491–518 (1990).

    Article  PubMed  Google Scholar 

  32. Schmidt D, Graner A: Genomic organization and sequence diversity of the long terminal repeat (LTR) of the BARE-1 retrotransposon family in barley. Barley Genet Newsl 24: 24–27 (1994).

    Google Scholar 

  33. Schwarzacher T, Leitch AR: Enzymatic treatment of plant material to spread chromosomes for in situ hybridizaton. In: Isaac PG (ed) Methods in Molecular Biology, pp. 153–160, Humana Press, Totawa, NJ (1994).

    Google Scholar 

  34. Smyth DR: Plant retrotransposons. In: Verma DPS (ed) Control of Plant Gene Expression, pp. 1–15. CRC Press, Boca Raton, FL (1993).

    Google Scholar 

  35. Smyth DR, Kalitsis P, Joseph JL, Sentry JW: Plant retrotansposons from Lilium henryi is related to Ty3 of yeast and the Gypsy group of Drosophila. Proc Natl Acad Sci USA 86: 5015–5019 (1989).

    PubMed  Google Scholar 

  36. Svitashev S, Bryngelsson T, Vershinin A, Pedersen C, Säll T, von Bothmer R: Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences. Theor Appl Genet 89: 801–810 (1994).

    Article  Google Scholar 

  37. Vander Wiel PL, Voytas DF, Wendel JF: Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.). J Mol Evol 36: 429–447 (1993).

    PubMed  Google Scholar 

  38. Varagona MJ, Purugganan M, Wessler SR: Alternative splicing induced by insertion of retrotransposons into the maize waxy gene. Plant Cell 4: 811–820 (1992).

    Article  PubMed  Google Scholar 

  39. Varmus HE: Retroviruses. In: Shapiro JA (ed) Mobile Genetic Elements, pp. 411–503. Academic Press, New York (1983).

    Google Scholar 

  40. Vershinin AV, Salina EA, Solovyov VV, Timofeyeva LL: Genomic organization, evolution, and structural peculiarities of highly repetitive DNA of Hordeum vulgare. Genome 33: 441–449 (1990).

    PubMed  Google Scholar 

  41. Vershinin AV, Salina EA, Svitashev SK: Is there a connection between genomic changes and wide hybridization? Hereditas 116: 213–217 (1992).

    PubMed  Google Scholar 

  42. Voytas DF, Cummings MP, Konieczny AK, Ausubel FM, Rodermel SR: Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89: 7124–7128 (1992).

    PubMed  Google Scholar 

  43. White SE, Habera LF, Wessler SR: Retrotransposons in the flanking regions of normal plant genes: A role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci USA 91: 11792–11796 (1994).

    PubMed  Google Scholar 

  44. Suoniemi A, Narvanto A, Schulman AH: The BARE retrotranspon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol (in press).

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Authors and Affiliations

  1. Institute of Biotechnology, University of Helsinki, Biocenter 1A, Viikinkaari 9, P.O. Box 56, FIN-00014, Helsinki, Finland

    Anu Suoniemi, Tiina Arna & Alan H. Schulman

  2. Agricultural Research Institute (RALA), Keldnaholti, IS-112, Reykjavík, Iceland

    Kesara Anamthawat-Jónsson

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  1. Anu Suoniemi
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  2. Kesara Anamthawat-Jónsson
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  3. Tiina Arna
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  4. Alan H. Schulman
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Suoniemi, A., Anamthawat-Jónsson, K., Arna, T. et al. Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol Biol 30, 1321–1329 (1996). https://doi.org/10.1007/BF00019563

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  • DOI: https://doi.org/10.1007/BF00019563

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