Genes & Genomics

, Volume 33, Issue 3, pp 251–257 | Cite as

Organization of the 5S rRNA gene units in Korean Lilium species

  • Sayeda Sultana
  • Jae-Wook BangEmail author
  • Hae-Woon ChoiEmail author
Research Article


The 5S rRNA gene unit was characterized from Lilium species distributed in Korea. Sequence analyses revealed that the 5S rDNA, harboring a highly conserved coding region (120 bp) and a divergent non transcribed spacer (NTS), ranged from 470 bp to 640 bp. The NTS regions showed length heterogeneity (350 bp–520 bp) due to the presence of several indels, and extensive sequence divergence among the species. Despite heterogeneity in length and nucleotide composition, the NTS regions possess some common features across the species, which include a T stretch region CTTTT and an identical motif of 11 bp (CAATGTATGAC) at the 3′ and 5′ flanking sequence of the coding region, respectively. These may play a role in the initiation and termination of transcription. The chromosomal distribution of the 5S rRNA gene was mapped on the long arm of chromosome 3 by fluorescence in situ hybridization (FISH). The phylogenetic analysis based on the NTS sequence broadly divided the Lilium species into two major groups which were referred to as the section Sinomartagon and Martagon by Comber’s classification of the genus Lilium. The present study showed that the 5S rDNA sequence was very useful to unravel the genetic relationships among Lilium species.


Lilium 5S rRNA gene NTS genetic variation FISH mapping 


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  1. Asano Y (1986) A numerical taxonomic study of the genus Lilium in Japan. J. Fac. Agr. Hokkaido Univ. 62: 333–341.Google Scholar
  2. Baker WJ, Hedderson TA and Dransfield J (2000) Molecular phylogenetics of Calamus (Palmae) and related rattan genera based on 5S nrDNA spacer sequence data. Mol. Phylogenet. Evol. 14: 218–221.PubMedCrossRefGoogle Scholar
  3. Baum BR, Bailey LG, Belyayev A, Raskina O and Nevo E (2004) The utility of the nontranscribed spacers of 5S rDNA units grouped into unit classes assigned to haplomes — a test on cultivated wheat and wheat progenitors. Genome 47: 590–599.PubMedCrossRefGoogle Scholar
  4. Baum BR and Bailey LG (1997) The molecular diversity of the 5S rRNA in Kengyilia alatavica (Drobov) J.L.Yang, Yen & Baum (Poaceae: Triticeae): potential genomic assignment of different rDNA units. Genome 40: 215–228.PubMedCrossRefGoogle Scholar
  5. Baum BR and Johnson DA (1996) The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analyses and phylogenetic relationships with 5S rDNA units of cultivated barley (H. vulgare L.). Genome 39: 140–149.PubMedCrossRefGoogle Scholar
  6. Baranova MV (1988) A synopsis of the system of the genus Lilium (Liliaceae). Bot. Zhur. 73: 1319–1329.Google Scholar
  7. Becerra JX (2003) Evolution of Mexican Bursera (Burseraceae) inferred from ITS, ETS, and 5S nuclear ribosomal DNA sequences. Mol. Phylogenet. Evol. 26:300–309.PubMedCrossRefGoogle Scholar
  8. Cloix C, Tutois S, Mathieu O, Cuvillier C, Espagnol MC, Picard G and Tourmente S (2000) Analysis of 5S rDNA arrays in Arabidopsis thaliana: physical mapping and chromosome specific polymorphism. Genome Res. 10: 679–690.PubMedCrossRefGoogle Scholar
  9. Comber HF (1949) A new classification of the genus Lilium. Lily Yearbook. Royal Hort. Soc. London.13: 86–105.Google Scholar
  10. Cronn RC, Zhou X, Paterson AH and Wendel JF (1996) Polymorphism and concerted evolution in a tandem repeated family: 5S ribosomal DNA in diploid and allopolyploid cottons. J. Mol. Evol. 42: 685–705.PubMedCrossRefGoogle Scholar
  11. De Jong PC (1974) Some notes on the evolution of lilies. Yearbook North American Lily Soc. 27: 23–28.Google Scholar
  12. Dubouzet JG and Shinoda K (1999a) Phylogenetic analysis of the internal transcribed spacer region of Japanese Lilium species. Theor. Appl. Genet. 98: 954–960.CrossRefGoogle Scholar
  13. Dubouzet JG and Shinoda K (1999b) ITS DNA sequence relationships between Lilium concolor Salisb., L. dauricum Ker-Gawl. and their putative hybrid, L. maculatum Thunb. Theor. Appl.Genet. 98: 213–218.CrossRefGoogle Scholar
  14. Felistocco E, Passeri V and Marconi G (2007) Investigations of 5S rDNA of Vitis vinifera L.: sequence analysis and physical mapping. Genome 50: 927–938.CrossRefGoogle Scholar
  15. Fukui K, Ohmido N and Khush GS (1994) Variability in rDNA loci in the genus Oryza detected through fluorescence in situ hybridization. Theor. Appl. Genet. 87: 893–899.CrossRefGoogle Scholar
  16. Goldsbrough RB, Ellis THN and Lomonosoff GD (1982) Sequence variation and methylation of the flax 5S RNA genes. Nucleic Acids Res. 10: 450–454.CrossRefGoogle Scholar
  17. Gottlob-McHugh SG, Levesque M, MacKenzie K, Oslon M, Yarosh O and Johnson DA (1990) Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plant. Genome 33:486–494.PubMedCrossRefGoogle Scholar
  18. Haruki K, Hosoki T, Nako Y and Ohta K (1997) Possibility of classification in some species of Lilium by PCR-RFLP of the ribulose-1, 5-bisphosphate carboxylase large subunit (rbcL) gene and ribosomal RNA gene. J. Japan Soc. Hort. Sci. 66: 189–192.CrossRefGoogle Scholar
  19. Haw SG (1986) The lilies of China. BT Batsford Ltd, London.Google Scholar
  20. Hayashi K and Kawano S (2000) Molecular systematics of Lilium and allied genera (Liliaceae): phylogenetic relationships among Lilium and related genera based on the rbcL and matK gene se quence data. Plant Species Biol. 15: 73–93.CrossRefGoogle Scholar
  21. Kim Y (1996) Lily industry and research, and native Lilium species in Korea. Acta Hort. (ISHS). 414: 69–80.Google Scholar
  22. Kim YS and Lee WB (1990) A study of morphological characters on the genus Lilium L. in Korea. Kor. J. Plant Tax. 20: 165–178.Google Scholar
  23. Korn LJ (1982) Transcription of Xenopus 5S ribosomal RNA genes. Nature 295: 101–105.PubMedCrossRefGoogle Scholar
  24. Lapitan NLV (1992) Organization and evolution of higher plant genomes. Genome 35: 171–181.CrossRefGoogle Scholar
  25. Lee SH, Choi HW, Sung JS and Bang JW (2010) Inter-genomic relationships among three medicinal herbs: Cnidium officinale, Ligusticum chuanxiong and Angelica polymorpha. Genes Genom. 32: 95–101.CrossRefGoogle Scholar
  26. Lee SH, Do GS and Seo BB (1999) Chromosomal localization of 5S rRNA gene loci and the implications for relationships within the Allium complex. Chromosome Res. 7: 89–93.PubMedCrossRefGoogle Scholar
  27. Lee WB, Choi SY and Kim YS (1993) An application of random amplified polymorphic DNA (RAPD) to systematics of some species of Lilium in Korea. Kor. J. Plant Tax. 23: 43–56.Google Scholar
  28. Lighty RW (1968) Evolutionary trends in lilies. Lily Yearbook. Royal Hort. Soc. London. 31: 40–44.Google Scholar
  29. Long EO and Dawid IB (1980) Repeated gene in eukaryotes. Ann. Rev. Biochem. 43: 727–764.CrossRefGoogle Scholar
  30. Mitchell RM (1998) Species DNA research report. NALS Q Bull. 52: 8–9.Google Scholar
  31. Negi MS, Rajagopal J, Chauhan N, Cronn and Lakshmikumaran (2002) Length and sequence heterogeneity in 5S rDNA of Populus deltoids. Genome 45:1181–1188.PubMedCrossRefGoogle Scholar
  32. Nishikawa T, Okazaki K and Nagamine T (2002) Phylogenetic relationships among Lilium auratum Lindley, L. auratum var. platyphyllum Baker and L. rubellum Baker based on three spacer regions in chloroplast DNA. Breed. Sci. 52: 207–213.CrossRefGoogle Scholar
  33. Nishikawa T, Okazaki K, Arakawa K and Nagamine T (2001) Phylogenetic analysis of section Sinomartagon in genus Lilium using sequences of the internal transcribed spacer region in nuclear ribosomal DNA. Breed. Sci. 51: 39–46.CrossRefGoogle Scholar
  34. Nishikawa T, Okazaki K, Uchino T, Arakawa K and Nagamine T (1999) A molecular phylogeny of Lilium in the internal transcribed spacer region of nuclear ribosomal DNA. J. Mol. Evol. 49: 238–249.PubMedCrossRefGoogle Scholar
  35. Noda, S (1986) Cytogenetic behavior, chromosomal differences, and geographic distribution in Lilium lancifolium (Liliaceae). Plant Species Biol. 1: 69–78.CrossRefGoogle Scholar
  36. Persson C (2000) Phylogeny of Neotropical Alibertia group (Rubiaceae), with emphasis on the genus Alibertia, inferred from ITS and 5S ribosomal DNA sequences. Amer. J. Bot. 87:1018–1028.CrossRefGoogle Scholar
  37. Prado EA, Faivre-Rampant P, Schneider C and Darmency MA (1996) Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species. Genome 39: 1020–1026.PubMedCrossRefGoogle Scholar
  38. Rešetnik I, Liber Z, Satovic Z, Cigić P and Nikolić T (2007) Molecular phylogeny and systematics of the Lilium carniolicum group (Liliaceae) based on nuclear ITS sequences. Plant Syst. Evol. 265: 45–58.CrossRefGoogle Scholar
  39. Rhee HK, Lim JH and Kim YJ (2005) Improvement of breeding efficiency for interspecific hybridization of lilies in Korea. Acta Hort. ISHS. 673: 107–112.Google Scholar
  40. Röser M, Winterfeld G, Grebenstein B and Hemleben V (2001) Molecular diversity and physical mapping of 5S rDNA in wild and cultivated oat grasses (Poaceae: Aveneae). Mol. Phylogenet. Evol. 21(2): 198–217.PubMedCrossRefGoogle Scholar
  41. Sastri DC, Hilu K, Appels R, Lagudah ES, Playford J and Baum BR (1992) An overview of evolution in plant 5S rDNA. Plant Syst. Evol. 183: 169–181.CrossRefGoogle Scholar
  42. Saini A and Jawali N (2009) Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications. Plant Syst. Evol. 280: 187–206.CrossRefGoogle Scholar
  43. Scoles GJ, Gill BX, Xin ZY, Clarke BC, McIntyre CL, Chapman C and Appels R (1988) Frequent duplications and deletion events in the 5S RNA genes and the associated spacer regions in the Triticeae. Plant Syst. Evol. 160:105–122.CrossRefGoogle Scholar
  44. Song NH and Seo BB (1988) Cytogenetics study of Lilium maximowiczii Regel using differential Giemsa stain. Res. Rev. Kyungpook Natl. Univ. 45: 63–68.Google Scholar
  45. Sultana S, Lee SH, Bang JW and Choi HW (2010) Physical mapping of rRNA gene loci and inter-specific relationships in wild Lilium distributed in Korea. J. Plant Biol. 53: 433–443.CrossRefGoogle Scholar
  46. Thompson JD, Higgings DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22: 4673–4680.PubMedCrossRefGoogle Scholar
  47. Trontin JF, Grandemange C and Favre JM (1999) Two highly divergent 5S rDNA unit size classes occur in composite tandem array in European larch (Larix decidua Mill.) and Japanese larch (L. kaempferi Lamb. Carr.). Genome 42: 837–848.PubMedGoogle Scholar
  48. Udovicic R, McFadden GI and Ladiges PY (1995) Phylogeny of Eucalyptus and Angophora based on 5S rDNA spacer sequence data. Mol. Phylogenet. Evol. 4: 247–256.PubMedCrossRefGoogle Scholar
  49. Volkov RA, Zanke C, Panchuk II and Hemleben V (2001) Molecular evolution of 5S rDNA of Solanum species (sect. Petota): application for molecular phylogeny and breeding. Theor. Appl. Genet. 103: 1273–1282.CrossRefGoogle Scholar
  50. Yamagishi M (1995) Detection of section-specific random amplified polymorphic DNA (RAPD) markers in Lilium. Theor. Appl. Genet. 91: 830–835.CrossRefGoogle Scholar
  51. Zanke C, Borisjuk N, Rouss B, Schilde-Rentschler L, Ninnemann H and Hemleben V (1995) A species specific oligonucleotide of the 5S rDNA spacer and species-specific elements identify symmetric somatic hybrids between Solanum tuberosum and S. pinnatisectum. Theor. Appl. Genet. 90: 720–72.CrossRefGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer Netherlands 2011

Authors and Affiliations

  1. 1.Department of Biology, College of Biological Science and BiotechnologyChungnam National UniversityDaejeonKorea

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