Molecular and General Genetics MGG

, Volume 250, Issue 3, pp 305–315

TheTy1-copia group retrotransposons inVicia species: copy number, sequence heterogeneity and chromosomal localisation

  • S. R. Pearce
  • D. Li
  • A. J. Flavell
  • G. Harrison
  • J. S. Heslop-Harrison
  • A. Kumar
Original Paper


We present an in-depth study of theTy1-copia group of retrotransposons within the plant genusVicia, which contains species with widely differing genome sizes. We have compared the numbers and sequence heterogeneities of these genetic elements in three diploidVicia species chosen to represent large (V. faba, 1C=13.3 pg), medium (V. melanops, 1C=11.5 pg) and small (V. sativa, 1C=2.3 pg) genomes within the genus. The copy numbers of the retrotransposons are all high but vary greatly, withV. faba containing approximately 106 copies,V. melanops about 1000 copies andV. sativa 5000 copies. The degree of sequence heterogeneity ofTy1-copia group elements correlates with their copy number within each genome, but neither heterogeneity nor copy number are related to the genome size of the host. In situ hybridization to metaphase chromosomes shows that the retrotransposons inV. faba are distributed throughout all chromosomes but are much less abundant in certain heterochromatic regions. These results are discussed in the context of plant retrotransposon evolution.

Key words

copia Vicia Retrotransposon Heterochromatin Plant 


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  1. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Phil Trans Roy Soc London B 274:227–274Google Scholar
  2. Boeke JD, Corces VG (1989) Transcription and reverse-transcription of retrotransposons. Annu Rev Microbiol 43:403–434Google Scholar
  3. Camirand A, St Pierre B, Martineau C, Brisson N (1990) Occurrence of acopia-like transposable element in one of the introns of the potato starch phosphorylase gene. Mol Gen Genet 224:33–39Google Scholar
  4. Carmena M, Gonzalez C (1995) Transposable elements map in a conserved pattern of distribution extending from β-heterochromatin to centromeres in Drosophila. Chromosoma, in pressGoogle Scholar
  5. Charlesworth B (1986) Genetic divergence between transposable elements. Genet Res (Camb) 48:111–118Google Scholar
  6. Dobel P, Schubert I, Rieger R (1973) Distribution of heterochromatin in a reconstructed karyotype ofVicia faba as identified by banding and DNA late replication patterns. Chromosoma 69:193–209Google Scholar
  7. Doolittle RF, Feng D (1990) Nearest neighbour procedure for relating progressively aligned amino acid sequences. Methods Enzymology 183:659–669Google Scholar
  8. Emori Y, Shiba T, Kanaya S, Inouye S, Yuki S, Saigo K (1985) Determination of the nucleotide sequences ofcopia andcopia-related RNA inDrosophila virus-like particles. Nature 315:773–776Google Scholar
  9. Feng DF, Doolittle RF (1990) Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol 183:375–387Google Scholar
  10. Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107Google Scholar
  11. Flavell AF, Smith D, Kumar A (1992a)Copia-Ty family retrotransposon heterogeneity in plants. Mol Gen Genet 231:233–242Google Scholar
  12. Flavell AF, Dumbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992b)Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20:3639–3644Google Scholar
  13. Flavell AF, Pearce SR, Kumar A (1994) Plant transposable elements and the genome. Curr Opin Genet Devel 4:838–844Google Scholar
  14. Fuchs J, Pich U, Meister A, Schubert I (1994) Differentiation of field bean heterochromatin by in situ hybridization with a repeatedFokI sequence. Chromsome Res 2:25–28Google Scholar
  15. Grandbastien M-A (1992) Retroelements in higher plants. Trends Genet 8:103–108Google Scholar
  16. Grandbastien M-A, Spielmann A, Caboche M (1989)Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337:376–380Google Scholar
  17. Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237–244Google Scholar
  18. Hirochika H, Hirochika R (1993)Ty1-copia retrotransposons as ubiquitous components of plant genomes. Jpn J Genet 68:35–46Google Scholar
  19. Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice. Mol Gen Genet 233:209–216Google Scholar
  20. Joseph JL, Sentry JW, Smyth DR (1990) Interspecies distribution of abundant DNA sequences inLilium. J Mol Evol 30:146–154Google Scholar
  21. Konieczny A, Voytas DF, Cummings MP, Ausubel FM (1991) A superfamily ofArabidopsis thaliana retrotransposons. Genetics 127:801–809Google Scholar
  22. Kononowicz AK (1986) Cytofluorometric analysis of changes of heterochromatin fraction during differentiation of root cells in two subspecies ofVicia faba. Biol zbl 105:69–83Google Scholar
  23. Leeton PJ, Smyth DR (1993) An abundant LINE-like element amplified in the genome ofLilium speciosum. Mol Gen Genet 237:97–104Google Scholar
  24. Lindauer A, Frazer D, Bruderlein M, Schmitt R (1993) Reverse transcriptase families and acopia-like retrotransposon in the green algaVolvox carteri. FEBS Lett 319:261–266Google Scholar
  25. Mannienen I, Schulman AH (1993)Bare-1, acopia-like retroelement in barley (Hordeum vulgare). Plant Mol Biol 22:829–864Google Scholar
  26. Maxted N (1993) A phenetic investigation ofVicia L. subgenusVicia (Leguminosae,Viciae) Bot J Linnean Soc 111:155–182Google Scholar
  27. McClintock B (1951) Chromosomal organisation and genic expression. Cold Spring Harbor Symp Quant Biol 16:13–47Google Scholar
  28. Moore G, Lucas H, Batty N, Flavell RB (1991a) A family of retrotransposons and associated genomic variation in wheat. Genomics 10:461–468Google Scholar
  29. Moore G, Cheung W, Schwarzacher T, Flavell RB (1991b)Bis 1, a major component of the cereal genome and a tool for studying genomic organisation. Genomics 10:469–476Google Scholar
  30. Mount SM, Rubin GM (1985) Complete nucleotide sequence of theDrosophila transposable elementcopia: homology betweencopia and retroviral proteins. Mol Cell Biol 5:1630–1638Google Scholar
  31. Ramsay G (1984) C-banding inVicia species. In: Chapman GP, Tarawali SA (eds) Systems for cytogenetic analysis inVicia faba L. Nijhoff/Junk, Dordrecht, The Netherlands, pp 28–39Google Scholar
  32. Rowland RE (1981) Chromosome banding and heterochromatin inVicia faba. Theor Appl Genet 60:277–280Google Scholar
  33. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018Google Scholar
  34. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New YorkGoogle Scholar
  35. Schmidt T, Kubis S, Heslop-Harrison JS (1995) Analysis and chromosomal localisation of retrotransposons in sugarbeet (Beta vulgaris L.): LINEs andTy1-copia-like elements as major components of the genome. Chromosome Res 3:335–345Google Scholar
  36. Schwarzacher T, Leitch AR, Heslop-Harrison JS (1994) DNA in situ hybridization-methods for light microscopy. In: Harris N, Oparka KJ (eds) Plant cell biology: a practical approach. Oxford University Press, Oxford, pp 127–155Google Scholar
  37. Sentry JW, Smyth DR (1989) An element with long terminal repeats and its variant arrangements in the genome ofLilium henryi. Mol Gen Genet 215:349–354Google Scholar
  38. Smyth DR (1993) Plant retrotransposons. In: Verma DPS (ed) Control of gene expression. CRC Press, Baton Range, pp 1–15Google Scholar
  39. Vanderwiel PL, Voytas D, Wendel JF (1993)copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.) J Mol Evol 36:429–447Google Scholar
  40. Varmus H, Brown P (1989) In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington DC, pp 53–108Google Scholar
  41. Vosa GC, Marchi P (1972) On the quinacrine fluorescence and Giemsa staining patterns of chromosomes ofVicia faba. Giorn Bot Ital 106:151–159Google Scholar
  42. Voytas DF, Ausubel FM (1988) Acopia-like transposable element family inArabidopsis thaliana. Nature 336:342–244Google Scholar
  43. Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992)copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128Google Scholar
  44. White SE, Hebara L, Wessler SR (1994) Retrotransposons in the flanking regions of normal plant genes: a role forcopia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci USA 91:11792–11796Google Scholar

Copyright information

© Springer-Verlag 1996

Authors and Affiliations

  • S. R. Pearce
    • 1
  • D. Li
    • 1
  • A. J. Flavell
    • 1
  • G. Harrison
    • 2
  • J. S. Heslop-Harrison
    • 2
  • A. Kumar
    • 3
  1. 1.Department of BiochemistryUniversity of DundeeDundeeUK
  2. 2.Karyobiology GroupJohn Innes Centre, Colney LaneNorwichUK
  3. 3.Cell and Molecular Genetics DepartmentScottish Crop Research Institute, InvergowrieDundeeUK

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