Chromosome Research

, Volume 16, Issue 7, pp 919–933

FISH mapping and molecular organization of the major repetitive sequences of tomato

  • Song-Bin Chang
  • Tae-Jin Yang
  • Erwin Datema
  • Joke van Vugt
  • Ben Vosman
  • Anja Kuipers
  • Marie Meznikova
  • Dóra Szinay
  • René Klein Lankhorst
  • Evert Jacobsen
  • Hans de Jong
Article

DOI: 10.1007/s10577-008-1249-z

Cite this article as:
Chang, SB., Yang, TJ., Datema, E. et al. Chromosome Res (2008) 16: 919. doi:10.1007/s10577-008-1249-z

Abstract

This paper presents a bird’s-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA]4, a microsatellite that also forms part of the pericentromeres, together with [GA]8, [GATA]4 and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer region.

Key words

Cot fluorescence in-situ hybridization heterochromatin repetitive DNA repetitive sequences Solanum lycopersicum tomato 

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Song-Bin Chang
    • 1
    • 2
  • Tae-Jin Yang
    • 3
  • Erwin Datema
    • 4
  • Joke van Vugt
    • 5
  • Ben Vosman
    • 4
  • Anja Kuipers
    • 6
  • Marie Meznikova
    • 7
  • Dóra Szinay
    • 1
  • René Klein Lankhorst
    • 8
  • Evert Jacobsen
    • 6
  • Hans de Jong
    • 1
    • 8
  1. 1.Wageningen University, Laboratory of GeneticsWageningenThe Netherlands
  2. 2.Department of AgronomyNational Taiwan UniversityTaipeiTaiwan
  3. 3.Department of Plant Science, College of Agriculture and Life ScienceSeoul National UniversitySeoulRepublic of Korea
  4. 4.Wageningen University and Research Centre, Plant Research InternationalWageningenThe Netherlands
  5. 5.Departement van Moleculaire biologie191 NCMLS Radboud Universiteit, NijmegenNijmegenThe Netherlands
  6. 6.Wageningen University, Laboratory of Plant BreedingWageningenThe Netherlands
  7. 7.Institute of BiophysicsCzech Academy of SciencesBrnoCzech Republic
  8. 8.Wageningen University, Centre for Biosystems GenomicsWageningenThe Netherlands

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