Abstract
The 5S rRNA gene in higher eukaryotes is organized into repeated units of tandem array that comprise a conserved 120-bp coding region and a non-transcribed spacer (NTS) of variable length with nucleotides. The allotetraploid genome ofAllium sacculiferum consists of two unknown diploids (2n=32). Analyses have not been successful toward clarifying the origin of each genome due to their similar chromosome morphology and unmatched C-banding patterns. We PCR-amplified the coding and NTS regions of its 5S rRNA genes, cloned them into vectors, and determined their DNA sequences. Interestingly, the aligned sequences of the NTS clones could be divided into two distinctive groups based on the existence of a 3-bp CCT insertion/deletion at the beginning of the NTS region. This feature makes it an important genetic marker for distinguishing the origin of theA. sacculiferum chromosomes. Furthermore, by applying fluorescencein situ hybridization, we located the 5S rRNA gene loci on Chromosomes 5, 7, 8, 9, and 14; their distribution is unique toA. sacculiferum. These data support the idea that one set of this genome has originated from a CCT-containing close relative --A. deltoid-fistulosum -- and that the NTS region may be used as a molecular marker for identifying parental lines for the allotetraploidityof A. sacculiferum.
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Literature Cited
Appels R, Gerlach WL, Dennis ES, Swift H, Peacock WJ (1980) Molecular and chromosomal organization of DNA sequences coding for the ribisomal RNAs in cereals. Chromosoma78: 293–311
Baum BR, Bailey LC (2001) The origin of A genome donor of wheats (Triticum: Poaveae) — A prospective based on the sequence variation of the 5S DNA gene units. Genet Resource Crop Evol51: 183–196
Baum BR, Johnson DA (1999) The 5S rRNA gene in wall barley (Hordeum murinum L sensu lato): Sequence variation among repeat units and relationship to the Y haplome in the genusHordeum (Porceae: Triticeae). Genome42: 852–866
Brown DD, Wensink PC, Jordan E (1972) A comparison of the ribosomal DNAs ofXenopus laevis andXenopus mulleri: The evolution of tandem genes. J Mol Biol63: 57–72
Campbell CS, Wojciechowski MF, Baldwin BG, Alice A, Donoghue MJ (1997) Persistent nuclear ribosomal DNA sequences polymorphism in theAmelanchier agamic complex (Rosaceae). Mol Biol Evol14: 81–90
Crisp MD, Gilmore, SR, Weston PH (1999) Phylogenetic relationships of two anomalous species ofPultenaea (Fabaceae: Mirbelieae), and description of a new genus. Taxon48: 701–704
Cronn RC, Zhao X, Paterson AH, Wendel JF (1996) Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol42: 685–705
Do CS, Seo BB (2000) Phylogenetic relationships amongAllium subg.Rhizihdeum species based on the molecular variation of 5S rRNA genes. Kor J Biol Sci4: 77–85
Do GS, Seo BB, Ko JM, Lee SH, Park JH, Kim IS, Song SD (1999) Analysis of somaclonal variation through tissue culture and chromosomal localization of rDNA sites by fluorescent in situ hybridization in wildAllium tuberosum and a regenerated variant. Plant Cell Tiss Org Cult57: 113–119
Dover GA (1982) Molecular Drive: A cohesive mode of species evolution. Nature299: 111–117
Flavell RB (1986) Repetitive DNA and chromosomes. Phil Trans Royal Soc London B Biol Sci312: 227–242
Fritsch RM, Friesen N (2002) Evolution, domestication and taxonomy.In HD Ravinovitch, L Currah, eds,Allium Crop Science: Recent Advances. CAB international, Wallingford, England, pp 5–27
Goldsborough PB, Ellis TH, Cullis CA (1981) Organization of the 5S RNA genes in flax. Nucl Acids Res9: 5895–5904
Hanahan D (1983) Studies on transformation ofEscherichia coli with plasmids. J Mol Biol166: 557–580
Kellogg EA, Appels R (1995) Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics140: 325–343
Klaas M (1998) Applications and impact of molecular markers on evolutionary and diversity studies in the genusAllium. Plant Bleed117: 297–308
Lapitan NLV, Canal MW, Tanksley SD (1989) Somatic chromosome karyotypes of tomato based on in situ hybridization of the TAGI satellite repeat. Genome32: 992–998
Lee SH, Do GS, Seo BB (1999) Chromosomal localization of 5S rRNA gene loci and the implications for relationships within theAllium complex. Chrom Res7: 89–93
Leitch IJ, Heslop-Harrison JS (1993) Physical mapping of four sites of 5S ribosomal DNA sequences and one site of the x-amylase 2 gene in barley (Hordeum vulgare). Genome36: 517–523
Lewin B (2004) Genes III. Prentice Hall, Pearson Education, Inc., Upper Saddle River, NJ, USA
Liu ZL, Zhang D, Wang XQ, Ma XF, Wang XR (2003) Intragenomic and interspecific 5S rDNA sequence variation in five Asian pines. Amer J Bot90: 17–24
Long EO, David IB (1980) Repetitive genes in eukaryotes. Annu Rev Biochem49: 727–764
Maluszynska J, Heslop-Harrison JS (1991) Localization of tandemly-repeated DNA sequences inArabidopsis thaliana. Plant J1: 159–166
Maughan PJ, Kolano BA, Maluszynska J, Coles ND, Bonifacio A, Rojas J, Coleman CE, Stevens MR, Fairbanks DJ, Parkinson SE, Jellen EH (2006) Molecular and cytological characterization of ribosomal RNA genes inChenopodium quinoa andChenopodium berlandieri. Genome49: 825–839
Mes THM, Fritsch RM, Pollner S, Bachmann SK (1999) Evolution of the chloroplast genome and polymorphic ITS regions inAllium subg. Melanocrommyum. Genome42: 237–247
Mascia PN, Rubenstein I, Philips RL, Wang AS, Xiang LZ (1981) Localization of the 5S rRNA genes and evidence for diversity in the 5S rRNA region of maize. Gene18: 7–20
Mukai Y, Endo TR, Grill BS (1990) Physical mapping of the 18S-26S rRNA multigene family in common wheat. J Hered81: 290–295
Mukai Y, Nagahara Y, Yamamoto M (1993) Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome35: 489–495
Park YK, Park HC, Park CH, Kim NS (2000) Chromosomal localization and sequence variation of 5S rRNA gene in fiveCapsicum species. Mol Cells10: 18–24
Reddy AD, Suh SB, Ghaffari R, Singh NJ, Kim DJ, Han JH, Kim KS (2003) Bioinformatics analysis of SARS proteins and molecular dynamics simulated structure of an alpha-helix motif. Bull Kor Chem Soce24: 899–900
Rogers SO, Bendich AJ (1987) Ribosomal gene in plants, variability in copy number and in the intergenic spacer. Plant Mol eBiol9: 509–520
Rogers SO, Bendich AJ (1988) Extraction of DNA from plant tissue,In SB Gelvin, RA Schilperoort, eds, Plant Molecular Manual A6. Kluwer Academic Publishers, Dordrecht, pp 1–10
Rogers SO, Honda S, Bendich AJ (1986) Variation in the ribosomal RNA genes among individuals ofVicia fava. Plant Mol Biol6: 339–345
Samson ML, Wegnez M (1984) The 5S ribosomal genes inDrosophila melanogaster species subgroup. Nucleotide sequence of a 5S unit fromDrosophila simulance andDrosophila teissieri. Nucl Acids Res12: 1003–1014
Seo BB, Kim HH (1989) Giemsa C-banded karyotypes in two diploid and two tetraploidAllium species. Kor J Bot32: 181–188
Specht T, Wolters J, Erdmann VA (1990) Compilation of 5S rRNA and 5S rRNA gene sequences. Nucl Acids Res18: 2215–2230
Thompson JD, Higgins DC, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res16: 486–499
Tronin J, Grandemange C, Favre J (1999) Two highly divergent 5S rDNA unit size classes occur in composite tandem array in European larch (Larix decidua Mill.) and Japanese larch (Larix kaempferi (Lamb) Carr.). Genome42: 837–848
Wendel JF, Schnabel A, Seelanan T (1995) Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci USA92: 280–284
Yoon H-S (2003) A floral meristem identity gene influences physiological and ecological aspect of floral organogenesis. J Plant Biol 46(4): 271–276
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Seo, j.H., Lee, B.H., Seo, B.B. et al. Identification of a Molecular Marker and Chromosome Mapping of the 5S rRNA Gene inAllium sacculiferum . J. Plant Biol. 50, 687–691 (2007). https://doi.org/10.1007/BF03030614
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DOI: https://doi.org/10.1007/BF03030614