Molecular Genetics and Genomics

, Volume 270, Issue 6, pp 524–532

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

  • A. Miura
  • M. Kato
  • K. Watanabe
  • A. Kawabe
  • H. Kotani
  • T. Kakutani
Original Paper

DOI: 10.1007/s00438-003-0943-y

Cite this article as:
Miura, A., Kato, M., Watanabe, K. et al. Mol Genet Genomics (2004) 270: 524. doi:10.1007/s00438-003-0943-y

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.

Keywords

Heterochromatin DNA methylation Genome organization 

Supplementary material

supp.pdf (20 kb)
Supplementary material (PDF 21 KB)

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • A. Miura
    • 1
  • M. Kato
    • 1
    • 2
  • K. Watanabe
    • 3
  • A. Kawabe
    • 1
  • H. Kotani
    • 4
  • T. Kakutani
    • 1
    • 2
    • 3
  1. 1.Department of Integrated GeneticsNational Institute of GeneticsMishimaJapan
  2. 2.The Graduate University of Advanced StudiesMishimaJapan
  3. 3.CREST, Japan Science and Technology CorporationTokyoJapan
  4. 4.Kazusa DNA Research InstituteKisarazuJapan

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