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Organization of the KpnI family of chromosomal distal-end satellite DNAs in Silene latifolia

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Abstract

The major satellite DNAs of the dioecious plant Silene latifolia are represented by the repetitive sequences X43.1, RMY1 and members of the SacI family, which are located at the distal ends of chromosomes. To characterize the satellite DNAs at the distal ends of the chromosomes in S. latifolia (Sl-distal-satDNA), we isolated a bacterial artificial chromosome clone (number 15B12) that contained multiple repeat sequences with KpnI restriction sites, and subcloned a portion of this sequence into a plasmid vector. Sequencing analysis confirmed that recognition or degenerate sites for KpnI were repeated 26 times at intervals of 310–324 bp in the inserted DNA. The phylogenetic tree that was constructed with the 26 KpnI repeat units contained clustered branches that were independent of the SacI family. It is clear that the KpnI repeat belongs to an Sl-distal-satDNA family that is distinct from the SacI family. We designated this family as "KpnI" after the restriction enzyme that does not have a site in the SacI family. Multi-colored fluorescent in situ hybridization was performed with the KpnI family and RMY1 probes under high stringency conditions. The results suggest that chromosome 7 is unique and that it carries the KpnI family at only one end.

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Acknowledgements

This work was supported by Grants-in-aid for Scientific Research to S. K. (No. 13016022) and S. M. (No. 13740469) from the Japanese Ministry of Education, Science, and Culture.

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Author notes

  1. Sachihiro Matsunaga

    Present address: Department of Biotechnology, Graduate School of Engineering, Osaka, Japan

  2. Fukashi Shibata

    Present address: Research Institute for Bioresources, Okayama University, Okayama, Japan

Authors and Affiliations

  1. Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-601, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan

    Yusuke Kazama, Sachihiro Matsunaga, Wakana Uchida & Shigeyuki Kawano

  2. Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan

    Ryuji Sugiyama & Shigeyuki Kawano

  3. Faculty of Education, Ehime University, Matsuyama, Japan

    Fukashi Shibata & Masahiro Hizume

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  1. Yusuke Kazama
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Correspondence to Yusuke Kazama.

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Kazama, Y., Sugiyama, R., Matsunaga, S. et al. Organization of the KpnI family of chromosomal distal-end satellite DNAs in Silene latifolia . J Plant Res 116, 317–326 (2003). https://doi.org/10.1007/s10265-003-0106-6

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