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Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.)

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Abstract

Members of a novel Master family of class II transposons were identified in the carrot genome. Two elements, 2.5 kb long DcMaster1 and 4.4 kb long DcMaster-a, are characterized by 22 bp imperfect terminal inverted repeats and by 3 bp target site duplications. GenBank search revealed that related elements are also present in Medicago truncatula, including a 5.1 kb element MtMaster-a. Both DcMaster-a and MtMaster-a contain open reading frames encoding for putative transposases with the complete DDE domain typical for plant class II transposable elements belonging to PIF/Harbinger superfamily, where the Master elements form a distinct group. Less than 10 copies of the DcMaster element containing the DDE domain are present in genomes of carrot and other Apiaceae, but more copies with internal deletions or insertions may occur. DcMaster elements were associated with putative coding regions in 8 of 14 identified insertion sites. PCR amplification of carrot genomic DNA using a primer complementary to TIRs of DcMaster gave products <400 bp in size. We speculate that these may all represent a MITE-like family of transposable elements that we named Krak, present in the carrot genome in at least 3,600 copies.

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Acknowledgements

We are grateful to Patrick Masson and Ahmet Ipek for their critical review and comments in this research, and to Douglas Senalik for his assistance. This work complied to current laws governing genetic experimentation in the U.S.

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Author notes

  1. Yuan-Yeu Yau

    Present address: Plant Gene Expression Center, U.S. Department of Agriculture, 800 Buchanan Street, Albany, CA, 94710, USA

Authors and Affiliations

  1. Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, 31-425, Krakow, Poland

    Dariusz Grzebelus

  2. USDA-ARS Vegetable Crops Research Unit and Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA

    Yuan-Yeu Yau & Philipp W. Simon

  3. Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA

    Yuan-Yeu Yau

Authors
  1. Dariusz Grzebelus
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  2. Yuan-Yeu Yau
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  3. Philipp W. Simon
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Corresponding author

Correspondence to Philipp W. Simon.

Additional information

Communicated by M.-A. Grandbastien

Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession numbers DQ250792 to DQ250807 and DQ353734 to DQ353752.

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Grzebelus, D., Yau, YY. & Simon, P.W. Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.). Mol Genet Genomics 275, 450–459 (2006). https://doi.org/10.1007/s00438-006-0102-3

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  • DOI: https://doi.org/10.1007/s00438-006-0102-3

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