Molecular organization of 5S rDNA of perennial ryegrass Lolium perenne L.

  • O. O. Ishchenko Dept. of Molecular Genetics and Biotechnology, Yuri Fedkovych National University of Chernivtsi, Ukraine, 58012, Chernivtsi, Kotsiubynski str., 2
  • I. I. Panchuk Dept. of Molecular Genetics and Biotechnology, Yuri Fedkovych National University of Chernivtsi, Ukraine, 58012, Chernivtsi, Kotsiubynski str., 2
DOI: https://doi.org/10.7124/visnyk.utgis.16.2.1054

Abstract

Aim. Ribosomal DNA (rDNA) is an important tool for molecular taxonomy and represents a convenient model for studying the evolution of repeated sequences. However, for many groups of angiosperms, 5S rDNA remains poorly studied, in particular for such a large group as the Poaceae (Gramineae) family. Accordingly, it was decided to analyze the molecular organization of 5S rDNA in the widespread and economically important species Lolium perenne. Methods. DNA extraction, PCR amplification, cloning and sequencing. Results. Two clones of L. perenne 5S rDNA were sequenced. It was shown that only one variant of 5S rDNA repeats with a 188–189 bp-long intergenic spacer (IGS) is present in the genome of L. perenne. Putative RNA polymerase III promoter elements were detected in the IGS. The level of IGS sequence similarity between representatives of different genera of the tribe Poeae ranges from 46 to 63 %. Conclusions. Comparison of IGS can be used to clarify the phylogenetic relationship between taxa of low ranks, in particular, between species and genera of the tribe Poeae.
Keywords: 5S rDNA, intergenic spacer, molecular evolution, Lolium, Poaceae.

References

Altschul S.F., Madden T.L., Schaffer A.A. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 1997. Vol. 25(17). P. 3389-3402.

Amosova A.V., Bolsheva N.L., Zoshchuk S.A. et al. Comparative molecular cytogenetic characterization of seven Deschampsia (Poaceae) species. PLOS One. 2017. Vol. 12(4). P. 1-17. doi: 10.1371/journal.pone.0175760.

Baum B.R., Bailey, L.G., Belyayev A. et al. The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes – a test on cultivated wheat and wheat progenitors. Genome. 2004. Vol. 47(3). P. 590–599. doi: 10.1139/g03-146

Baum B.R., Edwards T., Mamuti M., Johnson D.A. Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae). Genome. 2012. Vol. 55(3). P. 177-193. doi: 10.1139/g2012-006

Bolsheva N.L., Melnikova N.V., Kirov I.V. et al. Evolution of blue-flowered species of genus Linum based on high-throughput sequencing of ribosomal RNA genes. BMC Evol. Biol. 2017. Vol. 17(2). P. 23-36. doi: 10.1186/s12862-017-1105-x

Clayton W.D., Govaerts R., Harman K.T. et al. World checklist of Poaceae. Facilitated by the Royal Botanic Gardens, Kew: 2014. URL: http://apps.kew.org/wcsp/ – 2014

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.

Denk T., Grimm G. The oaks of western Eurasia: Traditional classifications and evidence from two nuclear markers. Taxon. 2010. Vol. 59(2). P. 351–366.

Douet J., Tourmente S. Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis. Heredity. 2007. Vol. 99(1). P. 5–13. doi: 10.1038/sj.hdy.6800964

Duvall M. R., Davis. J.I., Clark L.G. et al. Phylogeny of the Grasses (Poaceae) revisited. J. Syst. Evol. Bot. 2007. Vol. 23(1). P. 237-247. doi: 10.5642/aliso.20072301.18

Givnish T.J., Ames M., Mcneal J.R. et al. Assembling the tree of the monocotyledons: plastome sequence phylogeny and evolution of Poales. Ann. Miss. Bot. Gard. 2010. Vol. 97(4). P. 584-616. doi: 10.3417/2010023

Grimm G.W., Schlee M., Komarova N.Y. et al. Low-level taxonomy and intrageneric evolutionary trends in higher plants. Nova Acta Leopoldina NF. 2005. Vol. 92(342). P. 129-145.

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

Ishchenko O.O., Panchuk I.I., Andreev I.O. et al. Molecular organization of 5S ribosomal DNA of Deschapmpsia antarctica. Cytol. Genet. 2018. Vol. 52(6). P. 416-421. doi: 10.3103/S0095452718060105

Layat E., Saez-Vasquez J. Tourmente S. Regulation of Pol I-transcribed 45S rDNA and Pol III-transcribed 5S rDNA in Arabidopsis. Plant Cell Physiol. 2012. Vol. 53(2). P. 267-276. doi: 10.1093/pcp/pcr177

Mlinarec J., Franjevic D., Bockor L., Besendorfer V. Diverse evolutionary pathways shaped 5S rDNA of species of tribe Anemoneae (Ranunculaceae) and reveal phylogenetic signal. Bot. J. Linn. Soc. 2016. Vol. 182(1). P. 80-99. doi: 10.1111/boj.12452

Navrotska D., Andreev A., Betekhtin A. et al. Assessment of the molecular cytogenetic, morphometric and biochemical parameters of Deschampsia antarctica from its southern range limit in maritime Antarctic. Pol. Polar Res. 2018. Vol. 39(4). P. 525-248. doi: 10.24425/118759

Peng Y.Y., Wei Y.M., Baum B.R., Zheng Y.L. Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae). Genome. 2008. Vol. 51(2). P. 137–54. doi.org/10.1139/G07-111

Quintanar A., Castroviejo S., Catalan P. Phylogeny of the tribe Aveneae (Pooideae, Poaceae) inferred from plastid trnT-F and nuclear ITS sequences. Am. J. Bot. 2007. Vol. 94(9). P. 1554-1569. doi: 10.3732/ajb.94.9.1554

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

Roser M., Winterfeld G., Grebenstein B., Hemleben V. Molecular diversity and physical mapping of 5S rDNA in wild and cultivated oat grasses (Poaceae: Aveneae). Mol. Phylogen. Evol. 2001. Vol. 21(2). P. 198–217. doi: 10.1006/mpev.2001.1003

Rusak O.O., Petrashchuk V.I., Panchuk I.I., Volkov R.A. Molecular organization of 5S rDNA in two Ukrainian populations of Sycamore (Acer pseudoplatanus). The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2016. Vol. 14, No. 2. P. 216–20.

Saini A., Jawali N. Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications. Plant Syst. Evol. 2009. Vol. 280. P. 187-206. doi: 10.1007/s00606-009-0178-4.

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

Shelyfist A.Ie., Tynkevich Yu.O., Volkov R.A. Molecular organization of 5S rDNA Brunfelsia uniflora (Pohl.) D. Don. The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2018. Vol.16(1). P. 61-68.

Soreng R.J., Peterson P.M., Romschenko K. et al. A worldwide phylogenetic classification of the Poaceae (Gramineae). J. Syst. Evol. 2015. Vol. 53(2). P. 117–137. doi: 10.1111/jse.12150/epdf

Tynkevich Y.O., Nevelska A.O., Chorney I.I., Volkov R.A. Organization and variability of the 5S rDNA intergenic spacer of Lathyrus venetus. The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2015. Vol. 13(1). P. 81–87.

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

Tynkevich Yu.O., Volkov R.A. Novel structural class of 5S rDNA of Rosa wichurana Crep. Reports of the National Academy of Sciences of Ukraine. 2014. No. 5. P. 143-148.

Volkov A.R., Panchuk I.I. 5S rDNA of Dactylis glomerata (Poaceae): molecular organization and taxonomic application. The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2014. Vol. 12(1). P. 3–11.

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(8). P. 1273–1282. doi: 10.1007/s001220100670

Volkov R.A., Panchuk I.I., Borisjuk L.G., Borisjuk M.V. Plant rDNA: Organization, evolution, and using. Cytol. Genet. 2003. Vol. 37(1). P. 68–72.

Volkov R.A., Kozeretska I.A., Kyryachenko S.S. et al. Molecular evolution and variability of ITS1 and ITS2 in populations of Deschampsia antarctica from two regions of the Maritime Antarctic. Polar Sci. 2010. Vol. 4(3). P. 469-478. doi: 10.1016/j.polar.2010.04.011

Volkov R.A., Panchuk I.I., Borisjuk N.V. et al. Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna. BMC Plant Biol. 2017. Vol. 17(1). P. 1–15. doi: 10.1186/s12870-017-0978-6

Zeng Q., Chen H., Zhang C. et al. Definition of eight mulberry species in the genus Morus by internal transcribed spacer-based phylogeny. PLOS One. 2015. Vol. 10(8). P. 1-13. doi: 10.1371/journal.pone.0135411