Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L.
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.
KeywordsIGS 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.
- Barreneche T, Bahrman N, Kremer A (1996) Two dimensional gel electrophoresis confirms the low level of genetic differentiation between Quercus robur L. and Qurecus petraea (Matt.). Liebl For Genet 3:89–92Google Scholar
- Coart E, Lamote V, De Loose M, Van Bockstaele E, Lootens P, Roldan-Ruiz I (2002) AFLP markers demonstrate local genetic differentiation between two indigenous oak species (Quercus robur L. and Quercus petraea (Matt.) Liebl.) in Flemish populations. Theor Appl Genet 105:431–439PubMedCrossRefGoogle Scholar
- Cullis CA, Creissen GP, Gorman SW, Tiasdale RD (1988) The 25S, 18S and 5S ribosomal RNA genes from Pinus radiata D.Don. In: Cheliak WM, Yappa AA (eds) Molecular genetics of forest trees. Canadian Forest service, Petawawa National forest Institute, pp 34–40Google Scholar
- Samuel R, Pinsker W, Ehrendorfer F (1995) Electrophoretic analysis of genetic variation within and between populations of Quercus cerris, Q. pubescens, Q. petraea and Q. robur (Fagaceae) from eastern Austria. Bot Acta 108:290–299Google Scholar
- Schnare MN, Collings JC, Spencer DF, Gray MW (2000) The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences. Length heterogeneity, putative processing sites and potential interactions between U3 and small nucleolar RNA and the ribosomal precursor. Nucleic Acids Res 28:3452–3461PubMedCrossRefGoogle Scholar
- Suzuki H, Miyashita N, Moriwaki K, Kominami R, Muramatsu M, Kanehisa T, Bonhomme F, Petras ML, Ze-Chang Y, De-Yuan L (1986) Evolutionary implication of heterogeneity of the nontranscribed spacer region of ribosomal DNA repeating units in various subspecies of Mus musculus. Mol Biol Evol 3:126–137PubMedGoogle Scholar
- Zanetto A, Roussel G, Kremer A (1994) Geographic variation of inter-specific differentiation between Quercus robur L. and Quercus petraea (Matt.) Liebl. For Genet 99:111–123Google Scholar