Genes & Genomics

, 33:521 | Cite as

Dual-color FISH karyotype analyses using rDNAs in three Cucurbitaceae species

  • Nomar Espinosa Waminal
  • Nam-Soo Kim
  • Hyun Hee KimEmail author
Research Article


Dual-color fluorescence in situ hybridization (FISH) analysis of three Cucurbitaceae species from different genera was conducted using 5S and 45S rDNA probes. In Benincasa hispida (Thunb.) Cogn. (2n=24), the 45S rDNA probe hybridized on two chromosomes, one in the short arm of a medium-sized metacentric chromosome and another at the satellite of a chromosome. The 5S rDNA hybridized at a site proximal to the centromere of the same short arm of the 45S rRNA gene locus that occupied almost the entire short arm. For Citrullus lanatus (Thunb.) Matsum & Nakai (2n=22), the 45S rDNA probe hybridized at sites in the short arms of two chromosomes and the 5S rDNA probe was co-localized with the 45S rRNA locus at the region proximal to the centromere in one chromosome. The 45S rRNA loci occupied almost all of the short arms in both chromosomes. In Cucurbita moschata Duch. (2n=40), the 45S rDNA probe hybridized in five chromosomes in which the 45S rRNA genes occupied almost two-thirds of the chromosomes in two large chromosomes and the entire short arm of a medium-sized chromosome. Two other loci were present in two medium-sized chromosomes, one in the proximal region in the short arm of a chromosome and another at the tip of the long arm of a chromosome. Chromosomes of B. hispida were relatively larger than those of the other two species. The karyotype of B. hispida is composed of two metacentrics and 10 submetacentrics, while that of C. lanatus is composed of seven metacentrics and four submetacentrics and that of C. moschata is composed of 18 metacentrics and two submetacentrics. Comparative chromosome evolution among the three Cucurbitaceae species was attempted using the karyotypes and the chromosomal distribution patterns of the 5S and 45S rDNAs. The results presented herein will be useful in elucidating the phylogenetic relationships among Cucurbitaceae species, and will provide basic data for their breeding programs.


FISH Cucurbitaceae 5S and 45S rDNA Benincasa hispida Citrullus lanatus Cucurbita moschata 


  1. Bhaduri PN and Bose PC (1947) Cyto-genetical investigations in some common cucurbits, with special reference to fragmentation of chromosomes as a physical basis of speciation. J. Genet. 48: 237–256.PubMedCrossRefGoogle Scholar
  2. Chen JF, Staub JE, Adelberg JW and Jiang J (1999) Physical mapping of 45S rRNA genes in Cucumis species by fluorescence in situ hybridization. Can. J. Bot. 77: 389–393.Google Scholar
  3. Chung SM, Staub JE and Chen JF (2006) Molecular phylogeny of Cucumis species as revealed by consensus chloroplast SSR marker length and sequence variation. Genome 49: 219–229.PubMedCrossRefGoogle Scholar
  4. Coen ES and Dover GA (1983) Unequal exchanges and the coevolution of X and Y rDNA arrays in Drosophila melanogaster. Cell 33: 849–855.PubMedCrossRefGoogle Scholar
  5. Csordas A (1990) On the biological role of histone acetylation. Biochem. J. 265: 23–38.PubMedGoogle Scholar
  6. Darlington, CD and Wylie AP (1956) Chromosome atlas of flowering plants. George Allen and Unwin, Ltd, London.Google Scholar
  7. Datson PM and Murray BG (2006) Ribosomal DNA locus evolution in Nemesia: transposition rather than structural rearrangement as the key mechanism? Chromosome Res. 14: 845–857.PubMedCrossRefGoogle Scholar
  8. de Jong HJ, Fransz P and Zabel P (1999) High-resolution FISH in plants: techniques and applications. Trends Plant Sci. 4: 258–263.CrossRefGoogle Scholar
  9. de Melo NF and Guerra M (2003) Variability of the 5S and 45S rDNA sites in Passiflora L. species with distinct base chromosome numbers. Ann. Bot. 92: 309–316.PubMedCrossRefGoogle Scholar
  10. Dong F, Song J, Naess SK, Helgeson JP, Gebhardt C and Jiang J (2000) Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor. Appl. Genet. 101: 1001–1007.CrossRefGoogle Scholar
  11. Dover GA (1986) Molecular drive in multigene families; how biological novelities arise, spread, and assimilated. Trends Genet. 2: 159–165.CrossRefGoogle Scholar
  12. Dover GA (1989) Linkage disequilibrium and molecular drive in the rDNA gene family. Genetics 122: 249–252.PubMedGoogle Scholar
  13. Drouin G and Moniz de Sá M (1995) The concerted evolution of 5S ribosomal genes linked to the repeat units of other multigene families. Mol. Biol. Evol. 12: 481–493.PubMedGoogle Scholar
  14. Dubcovsky J and Dvorak J (1995) Ribosomal RNA multigene loci: nomads of the Triticeae genomes. Genetics 140: 1367–1377.PubMedGoogle Scholar
  15. Dutt B and Roy RP (1969) Cytogenetical studies in the interspecific hybrid of Luffa cylindrica L. and L. graveolens Roxb. Genetica 40: 7–18.CrossRefGoogle Scholar
  16. Dutt B and Roy RP (1971) Cytogenetic investigations in Cucurbitaceae I. Interspecific hybridization in Luffa. Genetica 42: 139–156.CrossRefGoogle Scholar
  17. Fukui K (2005) Recent development of image analysis methods in plant chromosome research. Cytogenet Genome Res. 109: 83–89.PubMedCrossRefGoogle Scholar
  18. Ganal M, Riede I and Hemleben V (1986) Organization and sequence analysis of two related satellite DNAs in cucumber (Cucumis sativus L.). J. Mol. Evol. 23: 23–30.CrossRefGoogle Scholar
  19. Gerlach WL and Bedbrook JR (1979) Cloning and characterization of ribosomal rDNA genes from wheat and barley. Nucleic Acids Res. 7: 1869–1885.PubMedCrossRefGoogle Scholar
  20. Han YH, Zhang ZH, Liu C, Liu J, Huang SW, Jiang JM and Jin WW (2009) Centromere repositioning in cucurbit species: implication of the genomic impact from centromere activation and inactivation. Proc. Natl. Acad. Sci. 106: 14937–14941.PubMedCrossRefGoogle Scholar
  21. Han YH, Zhang ZH, Liu JH, Lu JY, Huang SW and Jin WW (2008) Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization. Cytogenet. Genome Res. 122: 80–88.PubMedCrossRefGoogle Scholar
  22. Jeffrey C (2005) A new system of Cucurbitaceae. Bot. Zhurn. 90: 332–335.Google Scholar
  23. Kato A, Lamb JC and Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc. Natl. Acad. Sci. 101: 13554–13559.PubMedCrossRefGoogle Scholar
  24. Kirkpatrick KJ, Decker DS and Wilson HD (1985) Allozyme differentiation in the Cucurbita pepo complex: C. pepo var. medullosa vs. C. Texana. Econ. Bot. 39: 289–299.CrossRefGoogle Scholar
  25. Koo DH, Choi HW, Cho J, Hur Y and Bang JW (2005) A high-resolution karyotype of cucumber (Cucumis sativus L. ‘Winter Long’) revealed by C-banding, pachytene analysis, and RAPD-aided fluorescence in situ hybridization. Genome 48: 534–540.PubMedCrossRefGoogle Scholar
  26. Koo DH, Hur Y, Jin DC and Bang JW (2002) Karyotype analysis of a Korean cucumber cultivar (Cucumis sativus L. cv. Winter Long) using C-banding and bicolor fluorescence in situ hybridization. Mol. Cells 13: 413–418.PubMedGoogle Scholar
  27. Koo DH, Nam YW, Choi D, Bang JW, de Jong H and Hur Y (2010) Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences. Chromosome Res. 18: 325–336.PubMedCrossRefGoogle Scholar
  28. Kubista M, Åkerman B and Nordén B (1987) Characterization of interaction between DNA and 4′,6-diamidino-2-phenylindole by optical spectroscopy. Biochemistry 26: 4545–53.PubMedCrossRefGoogle Scholar
  29. Lamond AL and Earnshaw WC (1998) Structure and function in the nucleus. Science 280: 547–553.PubMedCrossRefGoogle Scholar
  30. Leitch IJ and Heslop-Harrison JS (1993) Physical mapping of sites of 5S rDNA sequences and one site of the α-amylase-2 gene in barley (Hordeum vulgare). Genome 36: 517–523.PubMedCrossRefGoogle Scholar
  31. Levan A, Fredga K and Sandberg AA (1964) Nomenclature for centromeric position on chromosomes. Hereditas 52: 201–220.CrossRefGoogle Scholar
  32. Levsky JM and Singer RH (2003) Fluorescence in situ hybridization: past, present and future. J. Cell Sci. 116: 2833–2838.PubMedCrossRefGoogle Scholar
  33. Li Q, Ma L, Huang J and Li L (2007) Chromosomal Localization of ribosomal DNA sites and karyotype analysis in three species of Cucurbitaceae (abstract only). Journal of Wuhan University, Natural Science ed., (DOI: CNKI:SUN:WHDY.0.2007-04-013)Google Scholar
  34. Lim KB, de Jong H, Yang TJ, Park JY, Kwon SJ, Kim JS, Lim MH, Kim JA, Jin M, Jin YM, et al. (2005) Characterization of rDNAs and tandem repeats in the heterochromatin of Brasicca rapa. Mol. Cells 19: 436–444.PubMedGoogle Scholar
  35. Long EO and Dawid IB (1980) Repeated genes in eukaryotes. Ann. Rev. Biochem. 49: 727–764.PubMedCrossRefGoogle Scholar
  36. Maluszynska J and Heslop-Harrison JS (1991) Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant. J. 1: 159–166.CrossRefGoogle Scholar
  37. Martins C and Galetti Jr. PM (1999) Chromosomal localization of 5S rDNA genes in Leporinus fish (Anostomidae, Characiformes). Chromosome Res. 7: 363–367.PubMedCrossRefGoogle Scholar
  38. Martins C and Wasko AP (2004) Organization and evolution of 5S ribosomal DNA in the fish genome. In Focus on Genome Research, Williams CR, ed., Nova Science Publishers, Inc. Hauppauge NY, pp. 335–363.Google Scholar
  39. Ng TJ (1993) New opportunities in the Cucurbitaceae. In New Crops, Janick J and Simon JE, eds., Wiley, New York pp. 538–546.Google Scholar
  40. Ohmido N, Fukui K and Kinoshita T (2010) Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). Proc. Jpn. Acad., Ser. B 86: 103–116.CrossRefGoogle Scholar
  41. Ramachandran C and Narayan RKJ (1990) Satellite DNA specific to knob heterochromatin in Cucumis metuliferus (Cucurbitaceae). Genetica 80: 129–138.CrossRefGoogle Scholar
  42. Raskana O, Belyayev A and Nevo E (2004) Activity of the En/Spm-like transpositions in meiosis as a bases of chromosome repatterning in a small, isolated, peripheral population of Aegilops spelotoides Tausch. Chromosome Res. 12: 153–161.CrossRefGoogle Scholar
  43. Ren Y, Zhang ZH, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H, et al. (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE 4: e5795.PubMedCrossRefGoogle Scholar
  44. Robinson RW and Decker-Walters DS (1999) Cucurbits. CAB International, Wallingford, Oxford, UK.Google Scholar
  45. Roussel P, André C, Comai L and Hernandez-Verdun D (1996) The rDNA transcription machinery is assembled during mitosis in active NORs and absent in inactive NORs. J. Cell. Biol. 133: 235–246.PubMedCrossRefGoogle Scholar
  46. Roy V, Monti-Dedieu L, Chaminade N, Sijak-Yakovlev S, Aulard S, Lemeunier F and Montchamp-Moreau C (2005) Evolution of the chromosomal location of rDNA genes in two Drosophila species subgroups: ananassae and melanogaster. Heredity 94: 388–395.PubMedCrossRefGoogle Scholar
  47. Sadder MT and Weber G (2001) Karyotype of maize (Zea mays L.) mitotic metaphase chromosomes as revealed by fluorescence in situ hybridization (FISH) with cytogenetic DNA markers. Plant Mol. Biol. Rep. 19: 117–123.CrossRefGoogle Scholar
  48. Schubert I and Wobus U (1985) In situ hybridization confirms jumping nucleolus organizing regions in Allium. Chromosoma (Berl) 92: 143–148.CrossRefGoogle Scholar
  49. Scoles GJ, Gill BS, Xin Z-Y, Clarke BC, Mcintyre CL, Chapman C and Appels R (1988) Frequent duplication and deletion events in the 5S RNA genes and the associated spacer regions of theTriticeae. Plant Syst. Evol. 160: 105–122.CrossRefGoogle Scholar
  50. Shishido R, Sano Y and Fukui K (2000) Ribosomal DNAs: an exception to the conservation of gene order in rice genomes. Mol. Gen. Genet. 263: 586–591.PubMedCrossRefGoogle Scholar
  51. Singh AK (1979) Cucurbitaceae and polyploidy. Cytologia 44: 897–905.CrossRefGoogle Scholar
  52. Singh M, Kumar R, Nagpure NS, Kushwaha B, Mani I, Chauhan UK and Lakra WS (2009) Population distribution of 45S and 5S rDNA in golden mahseer, Tor putitora: population-specific FISH marker. J. Genet. 88: 315–320.PubMedCrossRefGoogle Scholar
  53. Sumner AT (1990) Chromosome banding. London, Unwin Hyman.Google Scholar
  54. Vasconcelos S, Souza AA, Gusmão CL, Milani M, Benko-Iseppon AM and Brasileiro-Vidal AC (2010) Heterochromatin and rDNA 5S and 45S sites as reliable cytogenetic markers for castor bean (Ricinus communis, Euphorbiaceae). Micron 41: 746–753.PubMedCrossRefGoogle Scholar
  55. Wako T, Furushima-Shimogawara R, Belyaev ND, Turner BM and Fukui K (2002) Cell cycle dependent and lysine residue-specific dynamic changes of histone H4 acetylation in barley. Plant Mol. Biol. 49: 645–653.PubMedCrossRefGoogle Scholar
  56. Wako T, Murakami Y and Fukui K (2005) Comprehensive analysis of dynamics of histone H4 acetylation in mitotic barley cells. Genes Genet. Syst. 80: 269–276.PubMedCrossRefGoogle Scholar
  57. Wang X, He C, Moore SC and Ausio J (2001) Effects of histone acetylation on the solubility and folding of the chromatin fiber. J. Biol. Chem. 276: 12764–12768.PubMedCrossRefGoogle Scholar
  58. Whitaker TW (1933) Cytological and phylogenetic studies in the Cucurbitaceae. Bot. Gaz. 94: 780–790.CrossRefGoogle Scholar
  59. Wiegant J, Ried T, Nederlof PM, van der Ploeg M, Tanke HJ and Raap AK (1991) In situ hybridization with fluoresceinated DNA. Nucleic Acids Res. 19: 3237–3241.PubMedCrossRefGoogle Scholar
  60. Xu YH, Yang F, Cheng YL, Ma L, Wang JB and Li LJ (2007) Comparative analysis of rDNA distribution in metaphase chromosomes of Cucurbitaceae species. Hereditas (Beijing) 29: 614–620.CrossRefGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer Netherlands 2011

Authors and Affiliations

  • Nomar Espinosa Waminal
    • 1
  • Nam-Soo Kim
    • 2
  • Hyun Hee Kim
    • 1
    Email author
  1. 1.Plant Biotechnology Institute, Department of Life ScienceSahmyook UniversitySeoulKorea
  2. 2.Department of Molecular BiosciencesKangwon National UniversityChuncheonKorea

Personalised recommendations