Molecular Genetics and Genomics

, Volume 281, Issue 2, pp 207–221 | Cite as

Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L.

  • Nataša Bauer
  • Tomislav Horvat
  • Ivan Biruš
  • Vedrana Vičić
  • Vlatka Zoldoš
Original Paper


18S-5.8S-26S rDNA family comprises tandemly arranged, repeating units separated by an intergenic spacer (IGS) that contains transcription initiation/termination signals and usually repeating elements. In this study, we performed for the first time thorough sequence analysis of rDNA IGS region in two dominant European oaks, Quercus petraea and Q. robur, in order to investigate (1) if IGS sequence composition allows discrimination between these two species, and (2) if there is an rDNA length heterogeneity arising from IGS sequence. Two spacer length variants (slvs), 2 and 4 kb in length, were found in the genomes of both species. Inter-comparison of both slvs revealed no species-specificity in sequence or structural organization. Both slvs could be divided into four subregions; (1) the subrepeat region containing three repeated elements, (2) the AT-rich region containing matrix attachment sites and putative origin of replication, (3) the promoter region containing putative transcription initiation site and (4) the 5′ETS region. In the 4-kb slvs all four subregions are extended, and the subrepeat, AT-rich and promoter regions are duplicated. This is unique compared to other known IGS sequences where the variation in number of subrepeats is responsible for slvs creation. We also propose a possible evolutionary scenario to explain the formation of the subrepeat region in oak IGS. Results obtained in this work add to the previous picture of low-genetic differentiation of the two oaks and provide important data for further analyses of the function of IGS in control of rRNA gene expression.


IGS Spacer length variants rRNA genes Repetitive elements Quercus petraea Q. robur 



This work was funded by the Ministry of Science, Education and Sport of the Republic of Croatia, grants 119-1191196-1224 and 119-1191196-1225. We thank prof. Ž. Borzan for providing biological material.

Supplementary material

438_2008_404_MOESM1_ESM.pdf (276 kb)
Supplementary Tables and Figures (PDF 276 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Nataša Bauer
    • 1
  • Tomislav Horvat
    • 1
  • Ivan Biruš
    • 2
  • Vedrana Vičić
    • 1
  • Vlatka Zoldoš
    • 1
  1. 1.Faculty of Science, Department of Molecular BiologyUniversity of ZagrebZagrebCroatia
  2. 2.School of Medicine, DNA LaboratoryUniversity of OsijekOsijekCroatia

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