Skip to main content
SpringerLink
Log in

Application of 5S Ribosomal DNA for Molecular Taxonomy of Subtribe Loliinae (Poaceae)

  • Published:
Cytology and Genetics Aims and scope Submit manuscript

Abstract

The genus Festuca L. (subtribe Loliinae), which encompasses about 500 species, is one of the largest genera of the Poeae tribe and is distributed worldwide. The taxonomy of the genus Festuca and the subtribe Loliinae remains a subject of debate until now. Taking into account that the comparison of the 5S rDNA intergenic spacer (IGS) sequences is successfully used to estimate genetic distances between closely related plant taxa, we evaluated the possibility of its application in the study of the phylogeny of the Loliinae subtribe. Accordingly, we cloned and sequenced this region of F. ovina (subgenus Festuca) and F. carpatica (subgenus Leucopoa) genomes and compared them with the 5S rDNA of Lolium perenne and other members of the tribe Poeae. It was found that the genomes of F. ovina and F. carpatica contain only one structural class of 5S rDNA repeats. The level of IGS similarity between the two studied Festuca species ranges from 80.2 to 81.7%, and between these species and L. perenne—from 62.5 to 70.1%. Species of the genera Festuca and Lolium form a highly-supported monophyletic group on the phylodendrogram, which indicates their origin from a common ancestor. The high rate of the IGS evolution allows using of this nuclear genome region in studies on the molecular taxonomy of the subtribe Loliinae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.

Similar content being viewed by others

REFERENCES

  1. Andreev, I.O., Spiridonova, E.V., Kyryachenko, S.S., et al., Population-genetic analysis of Deschampsia antarctica from two regions of Maritime Antarctica, Moscow Univ. Biol. Sci. Bull., 2010, vol. 65, no. 4, pp. 208–210. https://doi.org/10.3103/S0096392510040243

    Article  Google Scholar 

  2. Barberá, P., Soreng, R.J., Peterson, P.M., et al., Molecular phylogenetic analysis resolves Trisetum (Poaceae: Pooideae: Koeleriinae) polyphyletic: evidence for a new genus, Sibirotrisetum and resurrection of Acrospelion, J. Syst. Evol., 2019, vol. 58, pp. 517–526.https://doi.org/10.1111/jse.12523

  3. Baum, B.R. and Johnson, D.A., Lophopyrum Á. Löve (1980), Thinopyrum Á. Löve (1980), Trichopyrum Á. Löve (1986): one, two or three genera? A study based on the nuclear 5S DNA, Genet. Resour. Crop. Evol., 1986, vol. 65, pp. 161–186. https://doi.org/10.1007/s10722-017-0519-z

    Article  Google Scholar 

  4. Catalán, P., Torrecilla, P., and Olmstead, R.G., Phylogeny of the festucoid grasses of subtribe Loliinae and allies (Poeae, Pooideae) inferred from ITS and trnL-F sequences, Mol. Phylogenet. Evol., 2004, vol. 31, pp. 517–542.https://doi.org/10.1016/j.ympev.2003.08.025

  5. Catalán, P., Torrecilla, P., Lypez-Rodríguez, J.A., et al., A systematic approach to subtribe Loliinae (Poaceae: Pooideae) based on phylogenetic evidence, Aliso, 2007, vol. 23, no. 1, pp. 380–405. https://doi.org/10.5642/aliso.20072301.31

    Article  Google Scholar 

  6. Cheng, Y., Zhou, K., Humphreys, M.W., et al., Phylogenetic relationships in the Festuca-Lolium complex (Loliinae; Poaceae): new insights from chloroplast sequences, Front. Ecol. Evol., 2016, vol. 4, p. 89. https://doi.org/10.3389/fevo.2016.00089

    Article  Google Scholar 

  7. Clayton, W.D. and Renvoize, S.A., Genera Graminum, in Grasses of the World, Kew Bull. Add. Ser., 1986, vol. 13, pp. 1–389.

  8. Cloix, C., Tutois, S., Mathieu, O., et al., Analysis of 5S rDNA arrays in Arabidopsis thaliana: physical mapping and chromosome-specific polymorphisms, Genome Res., 2000, vol. 10, no. 5, pp. 679–690. https://doi.org/10.1101/gr.10.5.679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Darbyshire, S.J., Realignment of Festuca subgenus Schedonorus with the genus Lolium (Poaceae), Novon, 1993, vol. 3, pp. 239–343.

    Article  Google Scholar 

  10. Davis, J.I. and Soreng, R.J., A preliminary phylogenetic analysis of the grass subfamily Pooideae (Poaceae), with attention to structural features of the plastid and nuclear genomes, including an intron loss in GBSSI, Aliso, 2007, vol. 23, pp. 335—348.

    Article  Google Scholar 

  11. Devesa, J.A., Catalán P, Muller, J., et al., Checklist de Festuca L. (Poaceae) en la Península Ibérica, Lagascalia, 2013, vol. 33, no. 1, pp. 183–274.

    Google Scholar 

  12. Duvall, M.R., Burke, S.V., and Clark, D.C., Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps, Bot. J. Linn. Soc., 2020, vol. 192, no. 1, pp. 9–20. https://doi.org/10.1093/botlinnean/boz060

    Article  Google Scholar 

  13. Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 2004, vol. 32, no. 5, pp. 1792–1797. https://doi.org/10.1093/nar/gkh340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Foggi, B., Scholz, H., and Valdés, B., The Euro Med treatment of Festuca (Gramineae)—new names and new combinations in Festuca and allied genera, Willdenowia, 2005, vol. 35, no. 2, pp. 241–244.https://doi.org/10.3372/wi.35.35202

  15. Garcia, S., Garnatje, T., and Kovarik, A., Plant rDNA database: ribosomal DNA loci information goes online, Chromosoma, 2012, vol. 121, no. 4, pp. 389–394. https://doi.org/10.1007/s00412-012-0368-7

    Article  CAS  PubMed  Google Scholar 

  16. Garcia, S., Wendel, J.F., Borowska-Zuchowska, N., et al., The utility of graph clustering of 5S ribosomal DNA homoeologs in plant allopolyploids, homoploid hybrids, and cryptic introgressants, Front. Plant Sci., 2020, vol. 11, p. 41. https://doi.org/10.3389/fpls.2020.00041

    Article  PubMed  PubMed Central  Google Scholar 

  17. Gaut, B.S., Tredway, L.P., Kubik, C., et al., Phylogenetic relationships and genetic diversity among members of the Festuca-Lolium complex (Poaceae) based on ITS sequence data, Plant Syst. Evol., 2000, vol. 224, pp. 33–53. https://doi.org/10.1007/BF00985265

    Article  CAS  Google Scholar 

  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. Missouri Bot. Gard., 2010, vol. 97, no. 4, pp. 584–616. https://doi.org/10.3417/2010023

    Article  Google Scholar 

  19. Hodkinson, T.R., Evolution and taxonomy of the grasses (Poaceae): a model family for the study of species-rich groups, Ann. Rev. Plant Biol., 2018, vol. 1, no. 1, pp. 255—294. https://doi.org/10.1002/9781119312994.apr0622

    Article  Google Scholar 

  20. Inda, L.A., Sanmartín, I., Buerki, S., et al., Mediterranean origin and Miocene-Holocene Old World diversification of meadow fescues and ryegrasses (Festuca subgenus Schedonorus and Lolium), J. Biogeogr., 2014, vol. 41, no. 3, pp. 600–614. https://doi.org/10.1111/jbi.12211

    Article  Google Scholar 

  21. Ishchenko, O.O., Panchuk, I.I., Andreev, I.O., et al., Molecular organization of 5S ribosomal DNA of Deschampsia antarctica, Cytol. Genet., 2018a, vol. 52, no. 6, pp. 416–421. https://doi.org/10.3103/S0095452719010146

  22. Ishchenko, O.O., Derevenko, T.O., and Panchuk, I.I., 5S rDNA of Timothy-grass Phleum pratense L., Sci. Her. Chernivtsi Univ. Biol. (Biol. Systems), 2018b, vol. 10, no. 2, pp. 107–112. https://doi.org/10.3186l/biosystems2018.02.107

  23. Ishchenko, O.O. and Panchuk, I.I., Molecular organization of 5S rDNA of perennial ryegrass Lolium perenne L., Bull. Vavilov Soc. Genet. Breed. Ukr., 2018c, vol. 16, no. 2, pp. 166–173.https://doi.org/10.7124/visnyk.utgis.16.2.1054

  24. Ishchenko, O.O., Mel’nyk, V.M., Parnikoza, I.Y., et al., Molecular organization of 5S ribosomal DNA and taxonomic status of Avenella flexuosa (L.) Drejer (Poaceae), Cytol. Genet., 2020, vol. 54, no. 6, pp. 505–513. https://doi.org/10.3103/S0095452720060055

    Article  Google Scholar 

  25. Kolano, B.M., Cann, J., Oskedra, M., et al., Parental origin and genome evolution of several Eurasian hexaploid species of Chenopodium (Chenopodiaceae), Phytotaxa, 2019, vol. 392, no. 3, pp. 163–185. https://doi.org/10.11646/phytotaxa.392.3.1

    Article  Google Scholar 

  26. Kopecký, D., Lukaszewski, A.J., and Doledžel, J., Cytogenetics of festulolium (Festuca x Lolium hybrids), Cytogen. Genom. Res., 2008, vol. 120, nos. 3–4, pp. 370–383. https://doi.org/10.1186/s12864-019-5766-2

    Article  Google Scholar 

  27. Krawczyk, K., Nobis, M., Nowak, A., et al., Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae), Sci. Rep., 2017, vol. 7, no. 1, pp. 1–11. https://doi.org/10.1038/s41598-017-11804-x

    Article  CAS  Google Scholar 

  28. Nani, T.F., Cenzi, G., Pereira, D.L., et al., Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution, Comp. Cytogenet., 2015, vol. 9, no. 4, pp. 645–660. https://doi.org/10.3897/CompCytogen.v9i4.5456

    Article  PubMed  PubMed Central  Google Scholar 

  29. Peng, Y.Y., Wei, Y.M., Baum, B.R., et al., Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae), Genome, 2008, vol. 51, no. 2, pp. 137–154. https://doi.org/10.1139/G07-111

    Article  CAS  PubMed  Google Scholar 

  30. Peterson, P.M., Romaschenko, K., Arrieta, Y.H., et al., A molecular phylogeny of the subtribe Sporobolinae and a classification of the subfamily Chloridoideae (Poaceae), Mem. NY Bot. Gard., 2017, vol. 118, pp. 127–151. https://doi.org/10.21135/893275341.003

    Article  Google Scholar 

  31. Porebski, S., Bailey, L.G., and Baum, B.R., Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components, Plant Mol. Biol. Rep., 1997, vol. 15, no. 1, pp. 8–15.https://doi.org/10.1007/BF02772108

  32. Rodrigues, J., Viegas, W., and Silva, M., 45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus, PLoS One, 2017, vol. 12, no. 4, e0176l70. https://doi.org/10.1371/journal.pone.0176 170

  33. Röser, M., Winterfeld, G., Grebenstein, B., et al., Molecular diversity and physical mapping of 5S rDNA in wild and cultivated oat grasses (Poaceae: Aveneae), Mol. Phylogen. Evol., 2001, vol. 21, no. 2, pp. 198–217. https://doi.org/10.1006/mpev.2001.1003

    Article  CAS  Google Scholar 

  34. Saarela, J.M., Liu, Q., Peterson, P.M., et al., Phylogenetics of the grass ‘Aveneae-type plastid DNA clade’ (Poaceae: Pooideae, Poeae) based on plastid and nuclear ribosomal DNA sequence data, in Diversity, Phylogeny, and Evolution in the Monocotyledons, Aarhus: Aarhus Univ. Press, 2010.

    Google Scholar 

  35. Saini, A. and Jawali, N., Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications, Plant Syst. Evol., 2009, vol. 280, nos. 3–4, pp. 187–206. https://doi.org/10.1007/s00606-009-0178-4

    Article  CAS  Google Scholar 

  36. Sambrook, J., Fritsch, E., and Maniatis, T., Molecular Cloning, New York: Cold Spring Harbor Laboratory, 1989.

    Google Scholar 

  37. Scoppola, A., Cardoni, S., Pellegrino, M., et al., Genetic diversity and taxonomic issues in Gastridium P. Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis, BioRxiv, 2019, 817965. https://doi.org/10.1101/817965

  38. Shelyfist, A.Y., Tynkevich, Y.O., and Volkov, R.A., Molecular organization of 5S rDNA of Brunfelsia uniflora (Pohl.) D. Don, Bull. Vavilov. Soc. Genet. Breed. Ukr., 2018, vol. 16, no. l, pp. 6l–68. https://doi.org/10.7124/visnyk.utgis.16.1.903

    Article  Google Scholar 

  39. Shelyfist, A.Y., Yakobyshen, D.V., and Volkov, R.A., Molecular structure of 5S rDNA of Mandragora autumnalis Bertol., Bull. Vavilov. Soc. Genet. Breed. Ukr., 2019, vol. 17, no. 2, pp. 187–195. https://doi.org/10.7124/visnyk.utgis.17.2.1220

    Article  Google Scholar 

  40. Simeone, M.C., Cardoni, S., Piredda, R., et al., Comparative systematics and phylogeography of Quercus section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation, Peer J., 2018, vol. 6, e5793. https://doi.org/10.7717/peerj.5793

    Article  PubMed  PubMed Central  Google Scholar 

  41. Simon, L., Rabanal, F.A., Dubos, T., et al., Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana, Nucleic Acids Res., 2018, vol. 46, no. 6, pp. 3019–3033. https://doi.org/10.1093/nar/ gkyl63

  42. Soreng, R.J., Davis, J.I., and Voionmaa, M.A., A phylogenetic analysis of Poaceae tribe Poeae sensu lato based on morphological characters and sequence data from three plastid-encoded genes: evidence for reticulation, and a new classification for the tribe, Kew Bull., 2007, vol. 62, no. 3, pp. 425–454.

    Google Scholar 

  43. Soreng, R.J., Peterson, P.M., Romschenko, K., et al., A worldwide phylogenetic classification of the Poaceae (Gramineae), J. Syst. Evol., 2015, vol. 53, no. 2, pp. 117–137. https://doi.org/10.1111/jse.12150

    Article  Google Scholar 

  44. Stamatakis, A., RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 2014, vol. 30, no. 9, pp. 1312–1313. https://doi.org/10.1093/bioinformatics/btu033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Thomas, H. and Humphreys, M.O., Progress and potential of interspecific hybrids of Lolium and Festuca, J. Agric. Sci., 1991, vol. 117, no. 1, pp. 1–8.

    Article  Google Scholar 

  46. Thomas, H.M., Morgan, W.G., and Humphreys, M.W., Designing grasses with a future-combining the attributes of Lolium and Festuca, Euphytica, 2003, vol. 133, no. 1, pp. 19–26. https://doi.org/10.1023/A:1025694819031

    Article  Google Scholar 

  47. Tkach, N., Schneider, J., Döring, E., et al., Phylogeny, morphology and the role of hybridization as driving force of evolution in grass tribes Aveneae and Poeae (Poaceae), BioRxiv, 2019, 707588. https://doi.org/10.1101/707588

  48. Torrecilla, P. and Catalán, P., Phylogeny of broad-leaved and fine-leaved Festuca lineages (Poaceae) based on nuclear ITS sequences, Syst. Bot., 2002, vol. 27, no. 2, pp. 241–251. https://doi.org/10.1043/0363-6445-27.2.241

    Article  Google Scholar 

  49. Tynkevich, Y.O. and Volkov, R.A., Structural organization of 5S ribosomal DNA in Rosa rugosa, Cytol. Genet., 2014, vol. 48, no. 1, pp. 1–6. https://doi.org/10.3103/S0095452714010095

    Article  Google Scholar 

  50. Tynkevich, Y.O. and Volkov, R.A., 5S Ribosomal DNA of distantly related Quercus species: molecular organization and taxonomic application, Cytol. Genet., 2019, vol. 53, no. 6, pp. 459–466. https://doi.org/10.3103/S0095452719060100

    Article  Google Scholar 

  51. Tynkevich, Y.O., Nevelska, A.O., et al., Organization and variability of the 5S rDNA intergenic spacer of Lathyrus venetus, Bull. Vavilov Soc. Genet. Breed. Ukr., 2015, vol. 13, no. 1, pp. 81–87.

    Google Scholar 

  52. Vaio, M., Mazzella, C., et al., Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae), Austral. J. Bot., 2019, vol. 67, no. 7, pp. 521–530. https://doi.org/10.1071/BT18236

    Article  CAS  Google Scholar 

  53. Volkov, A.R. and Panchuk, I.I., 5S rDNA of Dactylis glomerata (Poaceae): molecular organization and taxonomic application, Bull. Vavilov. Soc. Genet. Breed. Ukr., 2014, vol. 12, no. 1, pp. 3–11.

    Google Scholar 

  54. Volkov, R.A., Panchuk, I.I., et al., Plant rDNA: organization, evolution, and using, Cytol. Genet., 2003, vol. 37, no. 1, pp. 68–72.

    Google Scholar 

  55. 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, no. 3, pp. 469–478. https://doi.org/10.1016/j.polar.2010.04.011

    Article  Google Scholar 

  56. Wang, W., Chen, S., Guo, W., et al., Tropical plants evolve faster than their temperate relatives: a case from the bamboos (Poaceae: Bambusoideae) based on chloroplast genome data, Biotech. Biotech. Equip., 2020, vol. 34, no. 1, pp. 482–493. https://doi.org/10.1080/13102818.2020.1773312

    Article  CAS  Google Scholar 

  57. Yamada, T., Festuca, in Wild Crop Relatives: Genomic and Breeding Resources, Kole, C., Ed., Berlin: Springer, 2011, pp. 153–164.

    Google Scholar 

Download references

ACKNOWLEDGMENTS

The authors express their sincere gratitude to prof. Roman A. Volkov (Chernivtsi National University) for participating in the discussion of the results.

Funding

The research was supported by the Ministry of Education and Science of Ukraine (grant no. 0118U000137).

Author information

Authors and Affiliations

  1. Yuriy Fedkovych Chernivtsi National University, Ministry of Education and Science of Ukraine, 58012, Chernivtsi, Ukraine

    O. O. Ishchenko & І. І. Panchuk

  2. Institute of Ecology of the Carpathians, National Academy of Sciences of Ukraine, 79026, Lviv, Ukraine

    I. O. Bednarska

Authors
  1. O. O. Ishchenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. I. O. Bednarska
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. І. І. Panchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to І. І. Panchuk.

Ethics declarations

The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ishchenko, O.O., Bednarska, I.O. & Panchuk, І.І. Application of 5S Ribosomal DNA for Molecular Taxonomy of Subtribe Loliinae (Poaceae). Cytol. Genet. 55, 10–18 (2021). https://doi.org/10.3103/S0095452721010096

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.3103/S0095452721010096

Keywords:

Search

Navigation