The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers

Amar Kumar, Stephen R. Pearce, Karen McLean, Gill Harrison, J. S. Heslop-Harrison, Robbie Waugh, Andrew J. Flavell

    Research output: Contribution to journalArticle

    101 Citations (Scopus)

    Abstract

    The genomic organisation and diversity of the Ty1-copia group retrotransposons has been investigated in several crop plants and their relatives from both dicotyledonous and monocotyledonous families, including potato (Solanum tuberosum), faba beans (Vicia faba), Vicia melanops, Vicia sativa, barley (Hordeum vulgare), rye (Secale cereale), and onion (Allium cepa). Extreme heterogeneity in the sequence of the Ty1-copia retrotransposons from all these plant was revealed following sequence analysis of reverse transcriptase fragments. The estimated copy numbers of the Ty1-copia group retrotansposons for the genomes of S. tuberosum, L. esculentum, A. cepa, S. cereale, and V. faba is highly variable, ranging from a few hundred to approximately a million copies per genome. In situ hybridisation data from metaphase and prophase chromosomes of V. faba, S. cereale, and H. vulgare suggest that retrotransposon sequences are dispersed throughout the euchromatic regions of the genome but are almost undetectable in most heterochromatic regions. In contrast, similar data from metaphase chromosomes of A. cepa suggests that although retrotransposon sequences are dispersed throughout the euchromatic regions of the genome, they are predominantly concentrated in the terminal heterochromatin. These results are discussed in the context of the role played by the Ty1-copia group retrotransposons in the evolution of the plant genome. Lastly, the application of retrotransposon sequences as genetic markers for mapping genomes and for studying genetic biodiversity in plants is presented.

    Original languageEnglish
    Pages (from-to)205-217
    Number of pages13
    JournalGenetica
    Volume100
    Issue number1-3
    Publication statusPublished - Mar 1997

    Fingerprint

    Retroelements
    retrotransposons
    Vicia faba
    genomics
    genetic markers
    Onions
    Secale cereale
    Allium cepa
    Hordeum
    Solanum tuberosum
    genome
    Genome
    Metaphase
    metaphase
    Hordeum vulgare
    Vicia sativa
    Vicia
    Chromosomes, Human, 1-3
    chromosomes
    Plant Genome

    Keywords

    • Evolution
    • Genomic organisation
    • Molecular marker
    • Plants
    • Retroelements
    • Ty1-copia retrotansposons

    Cite this

    Kumar, A., Pearce, S. R., McLean, K., Harrison, G., Heslop-Harrison, J. S., Waugh, R., & Flavell, A. J. (1997). The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica, 100(1-3), 205-217.
    Kumar, Amar ; Pearce, Stephen R. ; McLean, Karen ; Harrison, Gill ; Heslop-Harrison, J. S. ; Waugh, Robbie ; Flavell, Andrew J. / The Ty1-copia group of retrotransposons in plants : genomic organisation, evolution, and use as molecular markers. In: Genetica. 1997 ; Vol. 100, No. 1-3. pp. 205-217.
    @article{f328b40544334a4d9384478df2340f12,
    title = "The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers",
    abstract = "The genomic organisation and diversity of the Ty1-copia group retrotransposons has been investigated in several crop plants and their relatives from both dicotyledonous and monocotyledonous families, including potato (Solanum tuberosum), faba beans (Vicia faba), Vicia melanops, Vicia sativa, barley (Hordeum vulgare), rye (Secale cereale), and onion (Allium cepa). Extreme heterogeneity in the sequence of the Ty1-copia retrotransposons from all these plant was revealed following sequence analysis of reverse transcriptase fragments. The estimated copy numbers of the Ty1-copia group retrotansposons for the genomes of S. tuberosum, L. esculentum, A. cepa, S. cereale, and V. faba is highly variable, ranging from a few hundred to approximately a million copies per genome. In situ hybridisation data from metaphase and prophase chromosomes of V. faba, S. cereale, and H. vulgare suggest that retrotransposon sequences are dispersed throughout the euchromatic regions of the genome but are almost undetectable in most heterochromatic regions. In contrast, similar data from metaphase chromosomes of A. cepa suggests that although retrotransposon sequences are dispersed throughout the euchromatic regions of the genome, they are predominantly concentrated in the terminal heterochromatin. These results are discussed in the context of the role played by the Ty1-copia group retrotransposons in the evolution of the plant genome. Lastly, the application of retrotransposon sequences as genetic markers for mapping genomes and for studying genetic biodiversity in plants is presented.",
    keywords = "Evolution, Genomic organisation, Molecular marker, Plants, Retroelements, Ty1-copia retrotansposons",
    author = "Amar Kumar and Pearce, {Stephen R.} and Karen McLean and Gill Harrison and Heslop-Harrison, {J. S.} and Robbie Waugh and Flavell, {Andrew J.}",
    year = "1997",
    month = "3",
    language = "English",
    volume = "100",
    pages = "205--217",
    journal = "Genetica",
    issn = "0016-6707",
    publisher = "Springer Verlag",
    number = "1-3",

    }

    Kumar, A, Pearce, SR, McLean, K, Harrison, G, Heslop-Harrison, JS, Waugh, R & Flavell, AJ 1997, 'The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers', Genetica, vol. 100, no. 1-3, pp. 205-217.

    The Ty1-copia group of retrotransposons in plants : genomic organisation, evolution, and use as molecular markers. / Kumar, Amar; Pearce, Stephen R.; McLean, Karen; Harrison, Gill; Heslop-Harrison, J. S.; Waugh, Robbie; Flavell, Andrew J.

    In: Genetica, Vol. 100, No. 1-3, 03.1997, p. 205-217.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - The Ty1-copia group of retrotransposons in plants

    T2 - genomic organisation, evolution, and use as molecular markers

    AU - Kumar, Amar

    AU - Pearce, Stephen R.

    AU - McLean, Karen

    AU - Harrison, Gill

    AU - Heslop-Harrison, J. S.

    AU - Waugh, Robbie

    AU - Flavell, Andrew J.

    PY - 1997/3

    Y1 - 1997/3

    N2 - The genomic organisation and diversity of the Ty1-copia group retrotransposons has been investigated in several crop plants and their relatives from both dicotyledonous and monocotyledonous families, including potato (Solanum tuberosum), faba beans (Vicia faba), Vicia melanops, Vicia sativa, barley (Hordeum vulgare), rye (Secale cereale), and onion (Allium cepa). Extreme heterogeneity in the sequence of the Ty1-copia retrotransposons from all these plant was revealed following sequence analysis of reverse transcriptase fragments. The estimated copy numbers of the Ty1-copia group retrotansposons for the genomes of S. tuberosum, L. esculentum, A. cepa, S. cereale, and V. faba is highly variable, ranging from a few hundred to approximately a million copies per genome. In situ hybridisation data from metaphase and prophase chromosomes of V. faba, S. cereale, and H. vulgare suggest that retrotransposon sequences are dispersed throughout the euchromatic regions of the genome but are almost undetectable in most heterochromatic regions. In contrast, similar data from metaphase chromosomes of A. cepa suggests that although retrotransposon sequences are dispersed throughout the euchromatic regions of the genome, they are predominantly concentrated in the terminal heterochromatin. These results are discussed in the context of the role played by the Ty1-copia group retrotransposons in the evolution of the plant genome. Lastly, the application of retrotransposon sequences as genetic markers for mapping genomes and for studying genetic biodiversity in plants is presented.

    AB - The genomic organisation and diversity of the Ty1-copia group retrotransposons has been investigated in several crop plants and their relatives from both dicotyledonous and monocotyledonous families, including potato (Solanum tuberosum), faba beans (Vicia faba), Vicia melanops, Vicia sativa, barley (Hordeum vulgare), rye (Secale cereale), and onion (Allium cepa). Extreme heterogeneity in the sequence of the Ty1-copia retrotransposons from all these plant was revealed following sequence analysis of reverse transcriptase fragments. The estimated copy numbers of the Ty1-copia group retrotansposons for the genomes of S. tuberosum, L. esculentum, A. cepa, S. cereale, and V. faba is highly variable, ranging from a few hundred to approximately a million copies per genome. In situ hybridisation data from metaphase and prophase chromosomes of V. faba, S. cereale, and H. vulgare suggest that retrotransposon sequences are dispersed throughout the euchromatic regions of the genome but are almost undetectable in most heterochromatic regions. In contrast, similar data from metaphase chromosomes of A. cepa suggests that although retrotransposon sequences are dispersed throughout the euchromatic regions of the genome, they are predominantly concentrated in the terminal heterochromatin. These results are discussed in the context of the role played by the Ty1-copia group retrotransposons in the evolution of the plant genome. Lastly, the application of retrotransposon sequences as genetic markers for mapping genomes and for studying genetic biodiversity in plants is presented.

    KW - Evolution

    KW - Genomic organisation

    KW - Molecular marker

    KW - Plants

    KW - Retroelements

    KW - Ty1-copia retrotansposons

    UR - http://www.scopus.com/inward/record.url?scp=0031453312&partnerID=8YFLogxK

    M3 - Article

    C2 - 9440274

    AN - SCOPUS:0031453312

    VL - 100

    SP - 205

    EP - 217

    JO - Genetica

    JF - Genetica

    SN - 0016-6707

    IS - 1-3

    ER -

    Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R et al. The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica. 1997 Mar;100(1-3):205-217.