Organization and polymorphysm of 5S rDNA intergenic spacer of blackthorn (Prunus spinosa L.)

  • Y. O. Tynkevich Yuri Fedkovych National University of Chernivtsi, Kotsiubynski str. 2, 58012 Chernivtsi, Ukraine
  • L. V. Kozub Yuri Fedkovych National University of Chernivtsi, Kotsiubynski str. 2, 58012 Chernivtsi, Ukraine
  • R. A. Volkov Yuri Fedkovych National University of Chernivtsi, Kotsiubynski str. 2, 58012 Chernivtsi, Ukraine


Aim. The 5S rDNA repeated units consist of conserved regions encoding 5S rRNA and variable intergenic spacers (IGS). The IGS sequences are commonly used as molecular markers for low-ranking phylogenetic, phylogeographical and microevolutionary studies. However, this genomic region still remains undescribed for the waist majority of genera in the Rosaceae family. Here we present the first report of the IGS molecular organization and polymorphism for the widespread member of the Rosaceae family, Prunus spinosa. Methods. PCR amplification, cloning and sequencing of 5S rDNA, bioinformatics analysis. Results. The 5SrDNA IGS of P. spinosa was cloned sequenced and compared with the IGS of three other representatives of the genus Prunus. It was found that the IGS variants present in the genome of P. spinosa differ by the number of subrepeats located at the 5’end. Each of these subrepeats contain RNA Pol III transcription termination signal. The IGS sequences of Prunus species evolved mainly by accumulation of nucleotide substitutions. The level of intragenomic similarity of P. spinosa IGS is 96.5-100%, while the similarity between the IGS of different Prunus species ranges from 73.0 to 87.3%. Conclusions. The IGS of 5S rDNA represents a useful marker for phylogenetic and taxonomic studies in the genus Prunus.
Keywords: 5S rDNA, molecular evolution, Prunus spinosa.


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