Abstract
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.
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References
Asano Y (1986) A numerical taxonomic study of the genus Lilium in Japan. J. Fac. Agr. Hokkaido Univ. 62: 333–341.
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.
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.
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.
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.
Baranova MV (1988) A synopsis of the system of the genus Lilium (Liliaceae). Bot. Zhur. 73: 1319–1329.
Becerra JX (2003) Evolution of Mexican Bursera (Burseraceae) inferred from ITS, ETS, and 5S nuclear ribosomal DNA sequences. Mol. Phylogenet. Evol. 26:300–309.
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.
Comber HF (1949) A new classification of the genus Lilium. Lily Yearbook. Royal Hort. Soc. London.13: 86–105.
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.
De Jong PC (1974) Some notes on the evolution of lilies. Yearbook North American Lily Soc. 27: 23–28.
Dubouzet JG and Shinoda K (1999a) Phylogenetic analysis of the internal transcribed spacer region of Japanese Lilium species. Theor. Appl. Genet. 98: 954–960.
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.
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.
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.
Goldsbrough RB, Ellis THN and Lomonosoff GD (1982) Sequence variation and methylation of the flax 5S RNA genes. Nucleic Acids Res. 10: 450–454.
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.
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.
Haw SG (1986) The lilies of China. BT Batsford Ltd, London.
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.
Kim Y (1996) Lily industry and research, and native Lilium species in Korea. Acta Hort. (ISHS). 414: 69–80.
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.
Korn LJ (1982) Transcription of Xenopus 5S ribosomal RNA genes. Nature 295: 101–105.
Lapitan NLV (1992) Organization and evolution of higher plant genomes. Genome 35: 171–181.
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.
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.
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.
Lighty RW (1968) Evolutionary trends in lilies. Lily Yearbook. Royal Hort. Soc. London. 31: 40–44.
Long EO and Dawid IB (1980) Repeated gene in eukaryotes. Ann. Rev. Biochem. 43: 727–764.
Mitchell RM (1998) Species DNA research report. NALS Q Bull. 52: 8–9.
Negi MS, Rajagopal J, Chauhan N, Cronn and Lakshmikumaran (2002) Length and sequence heterogeneity in 5S rDNA of Populus deltoids. Genome 45:1181–1188.
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.
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.
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.
Noda, S (1986) Cytogenetic behavior, chromosomal differences, and geographic distribution in Lilium lancifolium (Liliaceae). Plant Species Biol. 1: 69–78.
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.
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.
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.
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.
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.
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.
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.
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.
Song NH and Seo BB (1988) Cytogenetics study of Lilium maximowiczii Regel using differential Giemsa stain. Res. Rev. Kyungpook Natl. Univ. 45: 63–68.
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.
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.
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.
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.
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.
Yamagishi M (1995) Detection of section-specific random amplified polymorphic DNA (RAPD) markers in Lilium. Theor. Appl. Genet. 91: 830–835.
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.
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Sultana, S., Bang, JW. & Choi, HW. Organization of the 5S rRNA gene units in Korean Lilium species. Genes Genom 33, 251–257 (2011). https://doi.org/10.1007/s13258-010-0131-5
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DOI: https://doi.org/10.1007/s13258-010-0131-5