Orgfanization and variability of the 5S rDNA intergenic spacer of Lathyrus venetus

  • Y. O. Tynkevich Yuri Fedkovych National University of Chernivtsi, Ukraine, 58012, Chernivtsi, Kotsiubynski str., 2
  • A. O. Nevelska Yuri Fedkovych National University of Chernivtsi, Ukraine, 58012, Chernivtsi, Kotsiubynski str., 2
  • I. I. Chorney Yuri Fedkovych National University of Chernivtsi, Ukraine, 58012, Chernivtsi, Kotsiubynski str., 2
  • R. A. Volkov Yuri Fedkovych National University of Chernivtsi, Ukraine, 58012, Chernivtsi, Kotsiubynski str., 2


Aim. In populations of Lathyrus venetus (Mill.) Wohlf., which is an endangered species included in the Red Book of Ukraine, the majority of plants are hybrids between the original species and the related L. vernus. Therefore, the use of molecular markers, such as intergenic spacer region (IGS) of 5S rDNA, appears to be necessary for the assessment of genetic homogeneity of L. venetus populations and for development of a rational strategy of this species’ preservation. Methods. PCR amplification, cloning and sequencing of the 5S rDNA IGS of L. venetus. Results. It was found that two variants of 5S rDNA repeats are present in the genome of L. venetus. The IGS size is 158 and 162 bp, and the content of GC pairs amounts to 22,8–22,9 %. Typical for angiosperms RNA polymerase III promoter elements were detected in the IGS fragment preceding the 5S rRNA coding sequence. Among representatives of 17 genera of Fabaceae the highest level of IGS sequence similarity of 85,4–86,7 % was revealed between L. venetus and Pisum sativum, which belong to tribe Fabeae. Conclusions. High variability of the 5S rDNA IGS makes them a convenient molecular marker for elucidation of phylogenetic relationships between genera and species of tribe Fabeae.

Keywords: 5S rDNA, molecular markers, endangered species, Lathyrus.


Asmussen C., Liston A. Chloroplast DNA characters, phylogeny, and classification of Lathyrus species (Fabaceae). Am. J. Bot. 1998. Vol. 85(3). P. 387–401. doi: 10.2307/2446332

Крицька Л.І. Рід Lathyrus (Fabaceae) у флорі України. Укр. ботан. журн. 2014. Т. 71, № 6. С. 676–689.

Кагало О.О., Чорней І.І. Чина ряба, чина венеціанська (Lathyrus venetus (Mill.) Wohlf.). Червона книга України. Рослинний світ / за ред. Я.П. Дідуха. К.: Глобалконсалтинг, 2009. С. 473.

Cloix C., Tutois S., Mathieu O., Cuvillier C., Espagnol M.C., Picard G., Tourmente S. Analysis of 5S rDNA arrays in Arabidopsis thaliana: physical mapping and chromosome-specific polymorphisms. Genome Res. 2000. Vol. 10. P. 679–690. doi: 10.1101/gr.10.5.679

Volkov R.A., Zanke C., Panchuk I.I., Hemleben V. Molecular evolution of 5S rDNA of Solanum species (sect. Petota): application for molecular phylogeny and breeding. Theor. Appl. Genet. 2001. Vol. 103. P. 1273–1282. doi: 10.1007/s001220100670

Denk T., Grimm G. The oaks of western Eurasia: Traditional classifications and evidence from two nuclear markers. Taxon. 2010. Vol. 59. P. 351–366. doi: 10.1002/tax.592002

Coen E.S., Thoday J.M., Dover G. Rate of turnover of structural variants in the rDNA gene family of Drosophila melanogaster. Nature. 1982. Vol. 295. P. 564–568. doi: 10.1038/295564a0

Fulnecek J., Lim K.Y., Leitch A.R., Kovarik A., Matyasek R. Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species. Heredity. 2002. Vol. 88. P. 19–25. doi: 10.1038/sj.hdy.6800001

Rogers S.O., Bendich A.J. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. 1985. Vol. 5. P. 69–76. doi: 10.1007/BF00020088

Sambrook J., Fritsch E., Maniatis T. Molecular cloning. New York: Cold Spring Harbor Laboratory, 1989. 1626 p.

DNASTAR, 1998. MegAlign 3.18 edit. Software distributed by DNASTAR Inc., Madison, WI, USA.

Higgins D.G. Bleasby A.J. Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Bioinformatics. 1992. Vol. 8. P. 189–191. doi: 10.1093/bioinformatics/8.2.189

Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucl. Acids Res. 1997. Vol. 25. P. 3389–3402. doi: 10.1093/nar/25.17.3389

Douet J., Tourmente S. Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis. Heredity. 2007. Vol. 99. P. 5–13. doi: 10.1038/sj.hdy.6800964

Ellis T.H., Lee D., Thomas C.M., Simpson P.R., Cleary W.G., Newman M.-A., Burcham K.W. 5S rRNA genes in Pisum: sequence, long range and chromosomal organization. Mol. Gen. Genet. 1988. Vol. 214(2). P. 333–342. doi: 10.1007/BF00337732

Galian J.A., Rosato M., Rossello J.A. Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions. Syst. Biol. 2014. Vol. 63(2). P. 219–230. doi: 10.1093/sysbio/syt101

Gottlob-McHugh S.G., Levesque M., MacKenzie K., Olson M., Yarosh O., Jahnson D.A. Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants. Genome. 1990. Vol. 33(4). P. 486–494. doi: 10.1139/g90-072

Grimm G.W., Denk T. The reticulate origin of modern plane trees (Platanus, Platanaceae): A nuclear marker puzzle. Taxon. 2010. Vol. 59(1). P. 134–147. doi: 10.1002/tax.591014

Campell B.R., Song Y., Posch T.E., Cullis C.A., Town C.D. Sequence and organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana. Gene. 1992. Vol. 112. P. 225–228. doi: 10.1016/0378-1119(92)90380-8

Singh D., Ahuja P.S. 5S rDNA gene diversity in tea (Camellia sinensis (L.) O. Kuntze) and its use for variety identification. Genome. 2006. Vol. 49. P. 91–96. doi: 10.1139/g05-065

Tynkevich Y.O., Volkov R.A. Structural organization of 5S ribosomal DNA in Rosa rugosa. Cytol. Genet. 2014. Vol. 48(1). P. 1–6. doi: 10.3103/S0095452714010095

Takahata N., Kimura M. A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics. 1981. Vol. 98. P. 641–657.