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Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana

Molecular Genetics and Genomics volume 270, pages 524–532 (2004)Cite this article

Abstract

The differentiation between gene-rich and transposon-rich (gene-poor) regions is a common feature of plant genomes. This may be due to preferential integration of transposons into gene-poor regions or may be due to purifying selection against transposon insertion into gene-rich regions. We examined the distribution of a low-copy-number mobile subfamily of Arabidopsis CACTA transposons in the genomes of 19 natural variants (ecotypes) of A. thaliana, and compared that to the pattern of integrations induced in the laboratory by mutation of the DDM1 ( Decrease in DNA Methylation) gene. Sequences similar to mobile CACTA1 copies were distributed among the ecotypes and showed high degrees of polymorphism in genomic localization. Despite the high level of polymorphism, the copy number was low in all the ecotypes examined, and the elements were localized preferentially in pericentromeric and transposon-rich regions. This contrasts with the pattern of transposition induced by the ddm1 mutation, in which the range of integration sites is less biased and the copy number frequently increases. Based on these observations, we discuss the possible contribution of natural selection and chromatin structure to the distribution of transposons.

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Acknowledgements

We thank Y. Kinoshita, Y. Sasaki, and A. Terui for technical assistance, and T. Bureau and E. Richards for critical comments on the manuscript. We acknowledge the Arabidopsis Biological Stock Center at Ohio State University for the seed stocks. This work was supported by a Grant-in-Aid for Creative Scientific Research (No. 14GS0321)

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Affiliations

  1. Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, 411-8540 Shizuoka, Japan

    A. Miura, M. Kato, A. Kawabe & T. Kakutani

  2. The Graduate University of Advanced Studies, Yata 1111, Mishima, 411-8540 Shizuoka, Japan

    M. Kato & T. Kakutani

  3. CREST, Japan Science and Technology Corporation, 101-0062, Tokyo, Japan

    K. Watanabe & T. Kakutani

  4. Kazusa DNA Research Institute, Kisarazu, 291-0812 Chiba, Japan

    H. Kotani

Authors
  1. A. Miura
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  2. M. Kato
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  3. K. Watanabe
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  4. A. Kawabe
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  5. H. Kotani
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  6. T. Kakutani
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Corresponding author

Correspondence to T. Kakutani.

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Communicated by M.-A. Grandbastien

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Miura, A., Kato, M., Watanabe, K. et al. Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana . Mol Genet Genomics 270, 524–532 (2004). https://doi.org/10.1007/s00438-003-0943-y

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  • DOI: https://doi.org/10.1007/s00438-003-0943-y

Keywords

  • Heterochromatin
  • DNA methylation
  • Genome organization