Phylogenetic Relationships among Allium subg. Rhizirideum Species Based on the Molecular Variation of 5S rRNA Genes

  • Do, Geum-Sook (Department of Biology, College of Natural Sciences, Kyungpook National University) ;
  • Seo, Bong-Bo (Department of Biology, College of Natural Sciences, Kyungpook National University)
  • Published : 2000.03.01


This study has demonstrated the molecular variation of 5S rRNA genes in 15 Allium subgenus Rhizirideum and 1 Allium subg. Allium. For cloning of the 5S rRNA genes, PCR products were obtained from amplification with oligonucleotide primers which were derived from the conserved coding region of 5S rRNA genes. These amplified PCR products were cloned and identified by FISH and sequence analysis. The 5S rRNA loci were primarily located on chromosomes 5 and/or 7 in diploid species and various chromosomes in alloploid species. The size of the coding region of 5S rRNA genes was 120 bp in all the species and the sequences were highly conserved within Allium species. The sizes of nontranscribed spacer (NTS) region were varied from 194 bp (A. dektiude-fustykisum, 2n=16) to 483 bp (A. sativum). Two kinds of NTS regions were observed in A. victorialis var. platyphyllum a diploid, A. wakegi an amphihaploid, A. sacculiferum, A. grayi, A. deltoide-fistulosum and A. wenescens all allotetraploids, while most diploid species showed only one NTS region. The species containing two components of NTS region were grouped with different diploid species in a phylogenetic tree analysis using the sequences of 5S rRNA genes and adjacent non-coding regions.


  1. Altschul SF, Gish W, Miller W, Meyers EW, and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
  2. Appels R and Baum BR (1991) Evolution of the NOR and 5S DNA loci in the Triticeae. In: Doyle JJ and Solitis PS (eds), Plant Molecular Systematics, Chapman & Hall, New York, pp 92-116
  3. Bard A and Elkington T (1978) Numerical taxonomy of species in Allium subgenus Molium. New Phytol 81: 401-417
  4. Baum BR and Johnson DA (1994) The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare). Genome 37: 992-998
  5. Baum BR and Johnson DA (1998) The 5S rRNA gene in barley (Hordeum marinum Hudson sensu lato): sequence variation among repeat units and relationships to the X haplome in barley (Hordeum). Genome 41: 652-661
  6. Bradeen JM and Havey MJ (1995) Restriction fragment length polymorphisms reveal considerable nuclear divergence within a well-supported maternal clade in Allium section Cepa (Alliacea). Am J Bot 82: 1455-1462
  7. EI-Gadi A and Elkington T (1977) Numerical taxanomic studies on species in Allium subgenus Rhiziridium. New Phytol 79: 183-201
  8. Felsenstein J (1993) PHYLIP (Phylogeny inference package) version 3.5s. Department of Genetics, University of Washington, Seattle, Washington
  9. Friesen NV (1988) Lukovye sibiri. Sistematika, Kariologija, Chorologija. Novosibirsk, Nauka
  10. Gerlach WL and Dyer TA (1980) Sequence organization of the repeating units in the nucleus of wheat which contains 5S rRNA genes. Nucleic Acids Res 8: 4851-4865
  11. Hanahan D (1983) Studies on transformation of Esccherichia coli with plasmids. J Mol Biol 166: 557-580
  12. Hanelt P (1990) Allium taxonomy, evolution and history. In: Rabinowitch HD and Brewster JL (eds) Onions and Alied Crops Vol 1. Botany, Physiology and Genetics. CRC Press Inc. Boca Raton, pp 1-26
  13. Hanelt P, Schulze-Motel J, Fritsch RM, Kruse J, Maass HI, Ohle H, and Pistrick K (1992) Infrageneric grouping of Allium: The Gatersleben approach. In: Hanlet P, Hammer K, and Knuppfer H (eds), The genus Allium: taxanomic problems and genetic resources. Gatersleben, Hamburg, pp 107-123
  14. Havey MJ (1991) Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome. Theor Appl Genet 81: 752-757
  15. Hizume M (1994) Allodiploid nature of Allium wakegi Araki revealed by genomic in situ hybridization and localization of 5S and 18S rDNAs. Jpn J Genet 69: 407-415
  16. Kanazin V, Ananiev E, and Blake T (1993) The genetics of 5S rRNA encoding multigene families in barley. Genome 36: 1023-1028
  17. Khvyrleva TsD, Grazumyan K, and Ananev EV (1988) Organization and primary nucleotide sequence of the 5S rRNA genes in barley (Hordeum vulgare). Genetika 24: 1830-1840
  18. Kim HH, Kim JH, and Seo BB (1990) C-banded karyotypes of Allium victorialis, A. senescens, and A. senescens var. minor. Korean J Genet 12: 55-61
  19. Kolchinsky A, Kolesnikova M, and Ananiev EV (1991) Portraying of plant genomes using polymerase chain reaction amplification of ribosomal 5S genes. Genome 34: 1028-1031
  20. Korn LJ (1982) Transcription of Xenopus 5S ribosomal RNA genes. Nature 295: 101-105
  21. Lapitan NLV (1992) Organization and evolution of higher plant nuclear genomes. Genome 35: 171-181
  22. Lee SH and Seo BB (1997) Chromosomal localization of 5S and 18S-26S rRNA genes using fluorescence in situ hybridization in Allium wakegi. Korean J Genet 19: 19-26
  23. 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
  24. Linne von Berg G, Samoylov A, Klaas M, and Hanelt P (1996) Chloroplast DNA restriction analysis and the infrageneric grouping of Allium L. Plant Syst Evol 200: 253-261
  25. McCollum GD (1976) Onions and allies. In: Simmonds NW (ed) , Evolution of Crop Plants. Longman, London, pp 186-190
  26. Medlin H, Elwood HJ, Strickel S, and Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491-499
  27. Mes THM, Fritsch RM, Pollner S, and Bachmann K (1999) Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum. Genome 42: 237-247
  28. Mukai Y, Endo TR, and Gill BS (1990) Physical mapping of the 5S rRNA multigene family in common wheat. J Hered 81 : 290-295
  29. Pich U, Fritsch R, and Schubert I (1996) Closely related Allium species (Alliaceae) share a very similar satellite sequence. Plant Syst Evol 202: 255-264
  30. Rafalski JA, Wiewiorowski M, and Soli D (1982) Organization and nucleotide sequence of nuclear 5S rRNA genes in yellow lupin (Lupinus luteus). Nucleic Acids Res 10: 7635-7642
  31. Rogers SO and Bendich AJ (1988) Extraction of DNA from plant tissue. In: Glevin SB and Schilperoort RA (ed), Plant Molecular Biology Manual A6. Kluwer Academic Publishers, Dordrecht, pp 1-10
  32. Rouamba A, Ricroch A, and Sarr A (1993) Collecting onions germplasm in west Africa. FAO/BPRG Plant Genet Resou News 94/95: 15-17
  33. Sastri DC, Hilu K, Appels R, Lagudah ES, Playford J, and Baum BR (1992) An overview of evolution in plant 5S DNA. Plant Syst Evol 183: 169-181
  34. Schmidt T, Schwarzacher T, and Heslop-Harrison JS (1994) Physical mapping of rRNA gene by fluorescent in-situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgares). Theor Appl Genet 88: 629-636
  35. Selker EV, Morzycha-Wroblewska E, Steven JN, and Metzenberg RL (1986) An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes. Mol Gen Genet 205: 189-192
  36. Seo BB and Kim HH (1989) Giemsa C-banded karyotypes in two diploid and two tetraploid Allium species. Korean J Bot 32: 181-188
  37. Seo BB, Kim HH, and Kim JH (1989) Giemsa C-banded karyotypes and their relationship of four diploid taxa in Allium. Korean J Bot 32: 173-180
  38. Tashiro Y (1984) Genome analysis of Allium wakegi Araki. J Jpn Soc Hort Sci 52: 399-407
  39. Thompson JD, Higgins DG, and Gibson TJ (1994) CLUSTALW: improving the sensitivity of progresive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 22: 4673-4680
  40. Ved Brat S (1965) Genetic systems in Allium. Chromosoma 16: 486-499
  41. Venkateswarlu K, Lee S-W, and Nazor RN (1991) Conserved upstream sequence elements in plant 5S ribosomal RNA-encoding genes. Gene 105: 249-253