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Sequence Variation and Comparison of the 5S rRNA Sequences in Allium Species and their Chromosomal Distribution in Four Allium Species

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Abstract

The gene structure and sequence diversity of 5S rRNA genes were analyzed in 13 Allium species. While the lengths and sequences of the coding gene segments were conserved, the spacers were highly variable and could be characterized as either short (213–404 bp) or long (384–486 bp) spacers. The short spacers were further classified into five subtypes (SS-I to SS-V) and the long spacers into four subtypes (LS-I to LS-IV). The short spacers were more conserved than were the long spacers. There was a sequence duplication of 85 bp in SS-III that distinguished it from SS-II. The coding sequences of the 5S rRNA genes started with CGG and ended with either CCC or TCC. Both long and short spacers started with TTTT at their 5′-ends. However, the long spacers ended with a 3′-TGA sequence, whereas the short spacers terminated with various sequences, such as TTA, ATA, or TGA. GC content ranged from 27 to 41% in whole repeats, and the GC content in the long spacers was lower than in the short spacers. The nucleotide diversity in the coding regions was lower than in the spacers, and the nucleotide diversity in the coding regions did not correlate with that of the spacers. FISH analysis confirmed that each Allium species has either short spacers or long spacers. Although chromosomal locations of the 5S rRNA genes in Allium wakegi confirmed the allodiploid nature of A. cepa and A. fistulosum, spacer sequences revealed the absence of SS-II in A. cepa and in A. wakegi. The current study demonstrated that the 5S rRNA genes diverged in early stages in Allium species differentiation except of the allodiploid A. wakegi.

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References

  • Appel R, Honeycutt RL (1986) rDNA: evolution over a billion years. In: Dutta SK (ed) DNA systematic, vol II. CRC Press, Boca Raton, FL, pp 81–155

    Google Scholar 

  • Arnheim N (1983) Concerted evolution of multigene families. In: Nei M, Koehn RK (eds) Evolution of genes and proteins. Sinauer Associates, Sunderland, MA, USA, pp 36–61

    Google Scholar 

  • Bogdanov AA, Dontssova PA, Dokudovskaya SS, Lavrik IN (1995) Structure and function of 5S rRNA in the ribosome. Biochem Cell Biol 73:869–876

    Article  PubMed  CAS  Google Scholar 

  • Cloix C, Tutois S, Yukawa Y, Mathieu O, Cuvillier C, Espagnol MC, Picard G, Tourmente S (2000) Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogenous and only two of the genomic 5S loci produce mature 5S RNA. Genome Res 12:132–144

    Article  Google Scholar 

  • 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 Evol 42:685–705

    Article  PubMed  CAS  Google Scholar 

  • Drouin G, Moniz de Sa M (1995) The concerted evolution of 5S ribosomal genes linked to the repeat units of other multigene families. MolBiolEvol 12:481–493

    CAS  Google Scholar 

  • Dvořák J, Zhang HB, Kota RS, Lassner M (1989) Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species. Genome 32:1003–1016

    Article  Google Scholar 

  • Eickbush TH, Eickbush DG (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477–485

    Article  PubMed  CAS  Google Scholar 

  • Friesen N, Fritsch R, Blattner FR (2006) Phylogeny and new intragenic classification of Allium (Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso 22:372–395

    Google Scholar 

  • Fritsch RM, Blattner FR, Gurushidze M (2010) New classification of Allium L. Subg. Melanocrommyum (Webb &Berthel) Rouy (Alliaceae) based on molecular and morphological characters. Phyton 49:145–220

    Google Scholar 

  • Funari SS, Rapp G, Perbandt M, Dierks K, Vallazza M, Betzel C, Erdmann VA, Svergun DI (2000) Structure of free Thermus flavus 5S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering. J Biol Chem 275:31283–31288

    Article  PubMed  CAS  Google Scholar 

  • Harvey MJ (1995) Onion and other cultivated alliums. Allium spp. (Liliaceae). In Evolution of crop plants, Smartt J and Simmonds NW, eds., 2nd ed., Wiley Pub.Co. New York pp. 344–350

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Hori H, Osawa S (1986) Evolutionary change in the 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species. Biosystems 19:163–172

    Article  PubMed  CAS  Google Scholar 

  • Jeffrey AJ, Tamaki K, MacLeod A, Monckton DG, Neil DL, Armour JAL (1994) Complex gene conversion events in germline mutation at human minisatellites. Nat Genet 6:136–145

    Article  Google Scholar 

  • Kellogg E, Appels R (1995) Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics 140:325–343

    PubMed  CAS  Google Scholar 

  • Kim N-S, Kuspira J, Armstrong K, Bhambhini R (1993) Genetic and cytogenetic analyses of the A genome of Triticum monococcum. VIII. Localization of rDNAs and characterization of 5S rRNA genes. Genome 36:77–86

    Article  PubMed  CAS  Google Scholar 

  • Kiparisov S, Petrov A, Meskauskas A, Sergiev PV, Dintsova OA, Dinman JD (2005) Structural and functional analysis of 5S rRNA in Sacchromyces cereviceae. Mol Gen Genomics 274:235–247

    Article  CAS  Google Scholar 

  • Lee SH, Seo BB (1997) Chromosomal localization of 5S and 18S–26S rRNA genes using fluorescence in situ hybridization in Allium wakegi. Kor J Genet 19:19–26

    CAS  Google Scholar 

  • Lee SH, Do GS, Seo BB (1999) Chromosomal localization of 5S rRNA gene loci and implications for relationships within Allium complex. Chrom Res 7:89–93

    Article  PubMed  CAS  Google Scholar 

  • Li Q-Q, Zhou S-D, He X-J, Yu Y, Zhang Y-C, Wei X-Q (2010) Phylogeny and biogeography of Allium (Armaryllidaceae: Alliaceae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Annals Bot 106:709–733

    Article  CAS  Google Scholar 

  • Liu Z-L, Zhang D, Wang X-Q, Ma X-F, Wang X-R (2003) Intragenomic and intergenomic 5S rRNA sequence variation in five Asian pines. Am J Bot 90:17–24

    Article  PubMed  CAS  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    Article  PubMed  CAS  Google Scholar 

  • Nielson JN, Hallenburg C, Frederiksen S, Sørensen PD, Lombolt B (1993) Transcription of human 5S rRNA genes is influenced by an upstream DNA sequence. Nucleic Acids Res 21:3631–3636

    Article  Google Scholar 

  • Park YK, Park KC, Kim N-S (2000) Chromosomal localization and sequence variation of 5S rRNA gene in five Capsicum species. Mol Cells 10:18–24

    Article  PubMed  CAS  Google Scholar 

  • Park HM, Jeon EJ, Waminal NE, Shin KS, Kweon SJ, Park BS, Suh SS, Kim HH (2010) Detection of transgenes in three genetically modified rice lines by fluorescence in situ hybridization. Genes Genom 32:527–531

    Article  CAS  Google Scholar 

  • Ricroch A, Yockteng R, Brown SC, Nadot S (2005) Evolution of genome size across some cultivated Allium species. Genome 48:511–520

    Article  PubMed  CAS  Google Scholar 

  • Sanderson MJ, Doyle JJ (1992) Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. SystBiol 41:4–17

    Google Scholar 

  • Sastri DC, Hilu K, Appels R, Lagudah ES, Playford J, Baum BR (1992) An overview of evolution in plant 5S DNA. Pl Syst Evol 183:169–181

    Article  CAS  Google Scholar 

  • Schneeberger RG, Creissen GP, Cullis CA (1989) Chromosomal and molecular analysis of 5S RNA gene organization in the flax, Linum usitatissimum. Gene 83:75–84

    Article  PubMed  CAS  Google Scholar 

  • Scoles GJ, Gill BS, Xin Z-Y, Klarke BC, McIntyre CL, Chapman C, Appels R (1987) Frequent duplication and deletion events in the 5S RNA genes and the associated spacer regions of the Triticeae. Pl Syst Evol 160:105–122

    Article  Google Scholar 

  • Seo JH, Seo BB (2010) Independent chromosomal localization of two different 5S rDNA of Allium victorialis var. plathphyllum by sequential fluorescence in situ hybridization in accordance with sequence polymorphism. Genes Genom 32:129–135

    Article  CAS  Google Scholar 

  • Seo BB, Lee SH, Mukai Y (1997) Physical mapping of 5S and 18S–26S ribosomal RNA gene familes in Allium victorialis var. platyphyllum. J Plant Biol 40:132–137

    Article  CAS  Google Scholar 

  • Shibata F, Hizume M (2002) Evolution of 5S rDNA units and their chromosomal locations in Allium cepa and Allium schoenoprasum revealed by microdissection and FISH. Theor Appl Genet 105:167–172

    Article  PubMed  CAS  Google Scholar 

  • Smith MW, Meskaukas A, Wang P, Sergiev PV, Dinman JD (2001) Saturation mutagenesis of 5S rRNA in Saccharomyces cereviceae. Mol Cell Biol 21:8264–8275

    Article  PubMed  CAS  Google Scholar 

  • Son J-H, Park K-C, Kim T-W, Park Y-J, Kang J-H, Kim N-S (2010) Sequence diversification of 45S rRNA ITS, trnH-psbA spacer, and matK genic regions in several Allium species. Genes Genom 32:165–172

    Article  CAS  Google Scholar 

  • Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (2002) 5S ribosomal RNA database. Nucleic Acids Res 30:176–178

    Article  PubMed  CAS  Google Scholar 

  • Tashiro Y (1984) Genome analysis of Allium wakegi Araki. J Jpn Hort Sci 52:399–407

    Article  Google Scholar 

  • Tyler BM (1987) Transcription of Neurospora crassa 5S rRNA gene requires a TATA box and three internal elements. J Mol Biol 196:801–811

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This study was supported by the Bio-Green 21 Project (Grant 200804010340600080100) of the Rural Development Administration (RDA), Republic of Korea. JHS and SIL are the recipients of the BK21 Program supported by the Ministry of Education, Science and Technology (MEST), Republic of Korea. Authors express thanks to Dr. G. Fedak for critical reading of the manuscript.

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Authors and Affiliations

  1. Department of Molecular Biosciences, BK21 Training Team, Kangwon National University, Chuncheon, 200-701, South Korea

    Jae-Han Son, Sung-Il Lee & Nam-Soo Kim

  2. Institute of Biosciences and Biotechnology, Kangwon National University, Chuncheon, 200-701, South Korea

    Kyong-Cheul Park & Nam-Soo Kim

  3. Department of Life Science, Sahmyook University, Seoul, 139-742, South Korea

    Eun-Jin Jeon & Hyun-Hee Kim

Authors
  1. Jae-Han Son
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  2. Kyong-Cheul Park
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  3. Sung-Il Lee
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  4. Eun-Jin Jeon
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  5. Hyun-Hee Kim
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  6. Nam-Soo Kim
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Corresponding author

Correspondence to Nam-Soo Kim.

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J.-H. Son and K.-C. Park contributed equally to this work.

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Son, JH., Park, KC., Lee, SI. et al. Sequence Variation and Comparison of the 5S rRNA Sequences in Allium Species and their Chromosomal Distribution in Four Allium Species. J. Plant Biol. 55, 15–25 (2012). https://doi.org/10.1007/s12374-011-9185-4

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  • DOI: https://doi.org/10.1007/s12374-011-9185-4

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