Chromosome Research

, Volume 16, Issue 7, pp 919–933 | Cite as

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


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 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Arens P, Odinot P, van Heusden S, Lindhout P, Vosman B (1995) GATA- and GACA-repeats are not evenly distributed throughout the tomato genome. Genome 38: 84–90.PubMedGoogle Scholar
  2. Areshchenkova T, Ganal MW (1999) Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42: 536–544.PubMedCrossRefGoogle Scholar
  3. Arumuganathan K, Earle E (1991) Estimation of nuclear DNA content of plants by flow cytometry. Plant Mol Biol Rep. 9: 208–218.CrossRefGoogle Scholar
  4. Bennetzen JL (2000) The many hues of plant heterochromatin. Genome Biology 1: reviews 107.1–107.4.CrossRefGoogle Scholar
  5. Brandes A, Heslop-Harrison JS, Kamm A, Kubis S, Doudrick RL, Schmidt T (1997) Comparative analysis of the chromosomal and genomic organisation of Ty1-copia like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol Biol 33: 11–21.PubMedCrossRefGoogle Scholar
  6. Broun P, Tanksley SD (1996) Characterization and genetic mapping in simple repeat sequences in the tomato genome. Mol Gen Genet 250: 39–49.PubMedCrossRefGoogle Scholar
  7. Budiman MA, Mao L, Wood TC, Wing RA (2000) A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res 10: 129–136.PubMedGoogle Scholar
  8. Budiman MA, Chang SB, Lee S et al. (2004) Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor Appl Genet 108: 190–196.PubMedCrossRefGoogle Scholar
  9. Chang S-B (2004) Cytogenetic and molecular studies on tomato chromosomes using diploid tomato and tomato monosomic additions in tetraploid potato. PhD thesis. University of Wageningen.Google Scholar
  10. Copenhaver G, Nickel K, Kuromori T et al. (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286: 2468–2474.PubMedCrossRefGoogle Scholar
  11. Cuadrado A, Schwarzacher T (1998) The chromosomal organization of simple sequence repeats in wheat and rye genomes. Chromosoma 107: 587–594.PubMedCrossRefGoogle Scholar
  12. De Jong JH, Fransz P, Zabel P (1999) High resolution FISH in plants – techniques and applications. Trends Plant Sci 4: 258–262.CrossRefGoogle Scholar
  13. De Jong JH, Zhong X-B, Fransz PF, Wennekes-van Eden J, Jacobsen E, Zabel P (2000) High resolution FISH reveals the molecular chromosomal organisation of repetitive sequences of individual tomato chromosomes. In: Olmo E, Redi CA, eds. Chromosomes Today. Switserland: Birkhäuser Verlag, 13: 267–275.Google Scholar
  14. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8: 186–194.PubMedGoogle Scholar
  15. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175–185.PubMedGoogle Scholar
  16. Flavell AJ, Smith DB, Kumar A (1992) Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 231: 233–242.PubMedGoogle Scholar
  17. Ganal MW, Lapitan NLV, Tanksley SD (1988) A Molecular and Cytogenetic Survey of Major Repeated DNA Sequences in Tomato Lycopersicon esculentum. Mol Gen Genet 213: 262–268.CrossRefGoogle Scholar
  18. Ganal MW, Lapitan LV, Tanksley SD (1991) Macrostructure of the tomato telomeres. Plant Cell 3: 87–94.PubMedCrossRefGoogle Scholar
  19. Grandillo S, Tanksley SD (1995) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species L. pimpinellifolium. Theor Appl Genet 92: 935–951.CrossRefGoogle Scholar
  20. Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8: 570–575.PubMedCrossRefGoogle Scholar
  21. Jurka J (2005) GYPSODE1: Gypsy-type element from wild potato. Repbase Reports 5: 246.Google Scholar
  22. Khush GS, Rick CM (1968) Cytogenetic analysis of the tomato genome by means of induced deficiencies. Chromosoma 23: 452–484.CrossRefGoogle Scholar
  23. Kocsis E, Trus BL, Steer CJ, Bisher ME, Steven AC (1991) Image averaging of flexible fibrous macromolecules: the clathrin triskelion has an elastic proximal segment. J Struct Biol 107: 6–14.PubMedCrossRefGoogle Scholar
  24. Kuipers AGJ, Heslop-Harrison JS, Jacobsen E (1998) Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Genome 41: 357–367.PubMedCrossRefGoogle Scholar
  25. Lapitan NLV, Ganal MW, Tanksley SD (1989) Somatic chromosome karyotype of tomato based on in situ hybridization of the TGRI satellite repeat. Genome 32: 992–998.Google Scholar
  26. Lapitan NLV, Ganal MW, Tanksley SK (1991) Organization of the 5S ribosomal RNA genes in the genome of tomato. Genome 34: 509–514.Google Scholar
  27. Nagaki K, Cheng Z, Ouyang S et al. (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36: 138–145.PubMedCrossRefGoogle Scholar
  28. Pearce SR, Pich U, Harrison G et al. (1996a) The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res 4: 357–364.PubMedCrossRefGoogle Scholar
  29. Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ (1996b) The Ty1-copia group retrotransposons in Vicia species: copy number, sequence homogeneity and chromosomal localisation. Mol Gen Genet 250: 305–315.PubMedGoogle Scholar
  30. Peterson DG, Stack SM, Price HJ, Johnston JS (1995) Distribution of DNA in heterochromatin and euchromatin of Lycopersicon esculentum pachytene chromosomes. Tomato Genet Coop Rep 45: 35.Google Scholar
  31. Peterson DG, Price HJ, Johnston JS, Stack SM (1996) DNA content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes. Genome 39: 77–82.PubMedCrossRefGoogle Scholar
  32. Peterson DG, Pearson WR, Stack SM (1998) Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation. Genome 41: 346–356.CrossRefGoogle Scholar
  33. Peterson DG, Lapitan NLV, Stack SM (1999) Localization of single- and Low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH). Genetics 152: 427–439.PubMedGoogle Scholar
  34. Peterson DG, Schulze SR, Sciara EB et al. (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12: 795–807.PubMedCrossRefGoogle Scholar
  35. Ramanna MS, Prakken P (1967) Structure of and homology between pachytene and somatic metaphase chromosomes of the tomato. Genetica 38: 115–133.CrossRefGoogle Scholar
  36. Richards EJ, Ausubel FM (1988) Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 53: 127–136.CrossRefGoogle Scholar
  37. Schmidt T, Heslop-Harrison JS (1998) Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3: 195–199.CrossRefGoogle Scholar
  38. Schwartz S, Zhang Z, Frazer KA et al. (2000) PipMaker – A web server for aligning two genomic DNA sequences. Genome Res 10: 577–586.PubMedCrossRefGoogle Scholar
  39. Schweizer G, Ganal M, Ninnemann H, Hemleben V (1988) Species-specific DNA sequences for identification of somatic hybrids between Lycopersicon esculentum and Solanum acaule. Theor Appl Genet 75: 679–684.CrossRefGoogle Scholar
  40. Sherman JD, Stack SM (1995) Two-dimensional spreads of synaptonemal complexes from solanaceous plants. VI. High resolution recombination nodule map for tomato (Lycopersicon esculentum). Genetics 141: 683–708.PubMedGoogle Scholar
  41. Song J, Dong F, Lilly JW, Stupar RM, Jiang J (2001) Instability of bacterial artificial chromosome (BAC) clones containing tandemly repeated DNA sequences. Genome 44: 463–469.PubMedCrossRefGoogle Scholar
  42. Szinay D, Chang S-B, Khrustaleva L et al. (2008) High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. Plant J (in press).Google Scholar
  43. Tanksley SD, Ganal MW, Prince JP et al. (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160.PubMedGoogle Scholar
  44. Tilford CA, Kuroda-Kawaguchi T, Skaletsky H et al. (2001) A physical map of the human Y chromosome. Nature 409: 943–945.PubMedCrossRefGoogle Scholar
  45. Van Daelen RAJJ, Zabel P (1994) Preparation of high molecular weight plant DNA and analysis by pulsed field gel electrophoresis. In: Gelvin SB, Schilperoort RA, eds. Plant Molecular Biology Manual. Dordrecht: Kluwer Academic, H3: 1–21.Google Scholar
  46. Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley SD (2002) Deductions about the number, organization and evolution of genes in the tomato genome based on analysis of a large EST collection and selective genomic sequencing. Plant Cell 14: 1441–1456.PubMedCrossRefGoogle Scholar
  47. Vosman B, Arens P (1997) Molecular characterization of GATA/GACA microsatellite repeats in tomato. Genome 40: 25–33.PubMedCrossRefGoogle Scholar
  48. Vosman B, Arens P, Rus-Kortekaas W, Smulders MJM (1992) Identification of highly polymorphic DNA regions in tomato. Theor Appl Genet 85: 239–244.CrossRefGoogle Scholar
  49. Wallace RB, Johnson MJ, Hirose T, Miyake T, Kawashima EH, Itakura K (1981) The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequences to rabbit β-globin DNA. Nucleic Acids Res 9: 879–894.PubMedCrossRefGoogle Scholar
  50. Wang Y, Tang X, Cheng Z, Mueller L, Giovannoni J, Tanksley SD (2006) Euchromatin and pericentromere heterochromatin: comparative composition in the tomato genome. Genetics 172: 2529–2540.PubMedCrossRefGoogle Scholar
  51. Weide RJ, Hontelez J, van Kammen A, Koornneef M, Zabel P (1998) Paracentromeric sequences on tomato chromosome 6 show homology to human satellite III and to the mammalian CENP-B binding box. Mol Gen Genet 259: 190–197.PubMedCrossRefGoogle Scholar
  52. Wolters AMA, Schoenmakers HCH, van der Meulen-Muisers JJM et al. (1991) Limited DNA elimination from the irradiated potato parent in fusion products of albino Lycopersicon esculentum and Solanum tuberosum. Theor Appl Genet 83: 225–232.CrossRefGoogle Scholar
  53. Xu J, Earle ED (1994) Direct and sensitive fluorescence in situ hybridization of 45S rDNA on tomato chromosomes. Genome 37: 1062–1065.PubMedCrossRefGoogle Scholar
  54. Xu J, Earle ED (1996a) High resolution physical mapping of 45S (5.8S, 18S and 25S) rDNA gene loci in the tomato genome using a combination of karyotyping and FISH of pachytene chromosomes. Chromosoma 104: 545–550.PubMedCrossRefGoogle Scholar
  55. Xu J, Earle ED (1996b) Direct FISH of 5S rDNA on tomato pachytene chromosomes places the gene at the heterochromatic knob immediately adjacent to the centromere of chromosome 1. Genome 39: 216–221.PubMedCrossRefGoogle Scholar
  56. Yang TJ, Lee S, Chang SB, Yu Y, de Jong JH, Wing RA (2005) In depth sequence analysis of the centromeric region of tomato chromosome 12: Identification of a large CAA block and characterization of centromeric retrotranposons. Chromosoma 114: 103–117.PubMedCrossRefGoogle Scholar
  57. Zabel P, Meyer D, van de Stolpe O et al. (1985) Towards the construction of artificial chromosomes for tomato. In: van Vloten-Doting L, Groot GSP, Hall TC, eds. Molecular Form and Function of the Plant Genome. New York: Plenum, 609–624.Google Scholar
  58. Zamir D, Tanksley SD (1988) Tomato genome is comprised largely of fast-evolving, low copy-number sequences. Mol Gen Genet 213: 254–261.CrossRefGoogle Scholar
  59. Zhong XB, De Jong JH, Zabel P (1996) Preparation of tomato meiotic pachytene and mitotic metaphase chromosomes suitable for fluorescence in situ hybridization (FISH). Chromosome Res 4: 24–28.PubMedCrossRefGoogle Scholar
  60. Zhong XB, Fransz PF, Wennekes VEJ et al. (1998) FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato. Plant J 13: 507–517.PubMedCrossRefGoogle Scholar
  61. Zwick MS, Hanson RE, McKnight TD et al. (1997) A rapid procedure for the isolation of Cot-1 DNA from plants. Genome 40: 138–142.PubMedCrossRefGoogle Scholar

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

Personalised recommendations