Skip to main content
SpringerLink
Log in

The Use of Ribosomal DNA for Comparative Cytogenetics

  • Protocol
  • First Online:
Plant Cytogenetics and Cytogenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2672))

Abstract

Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA3 banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Sáez-Vásquez J, Delseny M (2019) Ribosome biogenesis in plants: from functional 45S ribosomal DNA organization to ribosome assembly factors. Plant Cell 31:1945–1967

    Article  PubMed  PubMed Central  Google Scholar 

  2. Sousa A, Bechteler J, Temsch EM, Renner SS (2020) Different from tracheophytes, liverworts commonly have mixed 35S and 5S arrays. Ann Bot 125:1057–1064

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Galian JA, Rosato M, Rosselló JA (2012) Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba. Heredity 108:640–646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Garcia S, Panero JL, Siroky J, Kovarik A (2010) Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family. BMC Plant Biol 10:176

    Article  PubMed  PubMed Central  Google Scholar 

  5. Rogers SO, Bendich AJ (1987) Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol 9:509–520

    Article  CAS  PubMed  Google Scholar 

  6. Garcia S, Kovařík A, Leitch AR, Garnatje T (2017) Cytogenetic features of rRNA genes across land plants: analysis of the plant rDNA database. Plant J 89:1020–1030

    Article  CAS  PubMed  Google Scholar 

  7. Kolano B, Siwinska D, McCann J, Weiss-Schneeweiss H (2015) The evolution of genome size and rDNA in diploid species of Chenopodium s.l. (Amaranthaceae). Bot J Linn Soc 179:218–235

    Article  Google Scholar 

  8. McGrath JM, Hickok LG (1999) Multiple ribosomal RNA gene loci in the genome of the homosporous fern Ceratopteris richardii. Can J Bot 77:1199–1202

    CAS  Google Scholar 

  9. Shibata F, Matsusaki Y, Hizume M (2016) A comparative analysis of multi–probe fluorescence in situ hybridization (FISH) karyotypes in 26 Pinus species (Pinaceae). Cytologia 81:409–421

    Article  CAS  Google Scholar 

  10. Rosato M, Kovařík A, Garilleti R, Rosselló JA (2016) Conserved organisation of 45S rDNA sites and rDNA gene copy number among major clades of early land plants. PLoS One 11:e0162544

    Article  PubMed  PubMed Central  Google Scholar 

  11. Schubert I, Anastassova-Kristeva M, Rieger R (1979) Specificity of NOR staining in Vicia faba. Exp Cell Res 120:433–435

    Article  CAS  PubMed  Google Scholar 

  12. Rosato M, Moreno-Saiz JC, Galián JA, Rosselló JA (2015) Evolutionary site–number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events. AoB Plants 7:plv35

    Article  Google Scholar 

  13. Volkov R, Medina F, Zentgraf U, Hemleben V (2004) Organization and molecular evolution of rDNA nucleolar dominance and nucleolus structure. In: Esser K, Luttge U, Beyschlag W, Murata J (eds) Progress in Botany, Springer-Verlag, Berlin Heidelberg, pp 106–146

    Google Scholar 

  14. Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 7:1869–1885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Komuro S, Endo R, Shikata K, Kato A (2013) Genomic and chromosomal distribution patterns of various repeated DNA sequences in wheat revealed by a fluorescence in situ hybridization procedure. Genome 56:131–137

    Article  CAS  PubMed  Google Scholar 

  16. Goriewa-Duba K, Duba A, Kwiatek M, Wiśniewska H, Wachowska U, Wiwart M (2018) Chromosomal distribution of pTa–535, pTa–86, pTa–713, 35S rDNA repetitive sequences in interspecific hexaploid hybrids of common wheat (Triticum aestivum L.) and spelt (Triticum spelta L.). PLoS One 13:e0192862

    Article  PubMed  PubMed Central  Google Scholar 

  17. Unfried I, Gruendler P (1990) Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana. Nucleic Acids Res 18:4011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Hajdera I, Siwinska D, Hasterok R, Maluszynska J (2003) Molecular cytogenetic analysis of genome structure in Lupinus angustifolius and Lupinus cosentinii. Theor Appl Genet 107:988–996

    Article  CAS  PubMed  Google Scholar 

  19. Kiss T, Kis M, Solymosy F (1989) Nucleotide sequence of a 25S rRNA gene from tomato. Nucleic Acids Res 17:796–796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Siroký J, Lysák MA, Dolezel J, Kejnovský E, Vyskot B (2001) Heterogeneity of rDNA distribution and genome size in Silene spp. Chromosom Res 9:387–393

    Article  Google Scholar 

  21. Choumane W, Heizmann P (1988) Structure and variability of nuclear ribosomal genes in the genus Helianthus. Theor Appl Genet 76:481–489

    Article  CAS  PubMed  Google Scholar 

  22. Benabdelmouna A, Abirached-Darmency M, Darmency H (2001) Phylogenetic and genomic relationships in Setaria italica and its close relatives based on the molecular diversity and chromosomal organization of 5S and 18S–5.8S–25S rDNA genes. Theor Appl Genet 103:668–677

    Article  CAS  Google Scholar 

  23. Paesold S, Borchardt D, Schmidt T, Dechyeva D (2012) A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome–arm identification, integration of genetic linkage groups and analysis of major repeat family distribution. Plant J 72:600–611

    Article  CAS  PubMed  Google Scholar 

  24. Gerlach WL, Dyer TA (1980) Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucleic Acids Res 8:4851–4865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Pedrosa A, Sandal N, Stougaard J, Schweizer D, Bachmair A (2002) Chromosomal map of the model legume Lotus japonicus. Genetics 161:1661–1672

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Schmidt T, Schwarzacher T, Heslop-Harrison JS (1994) Physical mapping of rRNA genes by fluorescent in–situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgaris). Theor Appl Genet 88:629–636

    Article  CAS  PubMed  Google Scholar 

  27. Besendorfer V, Krajačić-Sokol I, Jelenić S, Puizina J, Mlinarec J, Sviben T, Papeš D (2005) Two classes of 5S rDNA unit arrays of the silver fir, Abies alba Mill.: structure, localization and evolution. Theor Appl Genet 110:730–741

    Article  CAS  PubMed  Google Scholar 

  28. Waminal NE, Pellerin RJ, Kim NS, Jayakodi M, Park JY, Yang TJ, Kim HH (2018) Rapid and efficient FISH using pre–labeled oligomer probes. Sci Rep 8:8224

    Article  PubMed  PubMed Central  Google Scholar 

  29. He J, Lin S, Yu Z, Song A, Guan Z, Fang W, Chen S, Zhang F, Jiang J, Chen F, Wang H (2021) Identification of 5S and 45S rDNA sites in Chrysanthemum species by using oligonucleotide fluorescence in situ hybridization (Oligo–FISH). Mol Biol Rep 48:21–31

    Article  CAS  PubMed  Google Scholar 

  30. Schwarzacher T, Heslop-Harrison P (2000) Practical in situ Hybridization. BIOS Scientific Publishers, Oxford

    Google Scholar 

  31. Jenkins G, Hasterok R (2007) BAC ‘landing’ on chromosomes of Brachypodium distachyon for comparative genome alignment. Nat Protoc 2:88–98

    Article  CAS  PubMed  Google Scholar 

  32. Kwasniewska J, Jaskowiak J (2016) Transcriptional activity of rRNA genes in barley cells after mutagenic treatment. PLoS One 11:e0156865

    Article  PubMed  PubMed Central  Google Scholar 

  33. Tremetsberger K, Weiss-Schneeweiss H, Stuessy T, Samuel R, Kadlec G, Ortiz MÁ, Talavera S (2005) Nuclear ribosomal DNA and karyotypes indicate a NW African origin of South American Hypochaeris (Asteraceae, Cichorieae). Mol Phylogenet Evol 35:102–116

    Article  CAS  PubMed  Google Scholar 

  34. Feliner GN, Rossello JA (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species–level evolutionary studies in plants. Mol Phylogenet Evol 44:911–919

    Article  Google Scholar 

  35. Maddison WP, Maddison DR (2019) Mesquite: a modular system for evolutionary analysis. Version 3.61. http://www.mesquiteproject.org

  36. Revell LJ (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 3:217–223

    Article  Google Scholar 

  37. Vasconcelos EV, Vasconcelos S, Ribeiro T, Benko-Iseppon AM, Brasileiro-Vidal AC (2018) Karyotype heterogeneity in Philodendron s.l. (Araceae) revealed by chromosome mapping of rDNA loci. PLoS One 13:e0207318

    Article  PubMed  PubMed Central  Google Scholar 

  38. Zhou Y-P, Wang Z-X, Du Y-P, Li J-W, He H-B, Jia G-X (2020) Fluorescence in situ hybridization of 35S rDNA sites and karyotype of wild Lilium (Liliaceae) species from China: taxonomic and phylogenetic implications. Genet Resour Crop Evol 67:1601–1617

    Article  CAS  Google Scholar 

  39. Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320:481–483

    Article  CAS  PubMed  Google Scholar 

  40. Kolano B, McCann J, Orzechowska M, Siwinska D, Temsch E, Weiss-Schneeweiss H (2016) Molecular and cytogenetic evidence for an allotetraploid origin of Chenopodium quinoa and C. berlandieri (Amaranthaceae). Mol Phylogenet Evol 100:109–123

    Article  CAS  PubMed  Google Scholar 

  41. Weiss-Schneeweiss H, Bloch C, Turner B, Villasenor JL, Stuessy TF, Schneeweiss GM (2012) The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae). Evolution 66:211–228

    Article  CAS  PubMed  Google Scholar 

  42. Fredotović Ž, Šamanić I, Weiss-Schneeweiss H, Kamenjarin J, Jang T-S, Puizina J (2014) Triparental origin of triploid onion, Allium × cornutum (Clementi ex Visiani, 1842), as evidenced by molecular, phylogenetic and cytogenetic analyses. BMC Plant Biol 14:24

    Article  PubMed  PubMed Central  Google Scholar 

  43. Kovarik A, Dadejova M, Lim YK, Chase MW, Clarkson JJ, Knapp S, Leitch AR (2008) Evolution of rDNA in Nicotiana allopolyploids: a potential link between rDNA homogenization and epigenetics. Ann Bot 101:815–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Zozomová-Lihová J, Mandáková T, Kovaříková A, Mühlhausen A, Mummenhoff K, Lysak MA, Kovařík A (2014) When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine × schulzii trigenomic allopolyploid. New Phytol 203:1096–1108

    Article  PubMed  Google Scholar 

  45. Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z, Leitch AR (2008) Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS One 3:e3353

    Article  PubMed  PubMed Central  Google Scholar 

  46. Grunenwald H (2003) Optimization of polymerase chain reactions. In: Bartlett JMS, Stirling D (eds) PCR protocols. Humana Press, Totowa, pp 89–99

    Google Scholar 

  47. Liu ZL, Zhang D, Hong DY, Wang XR (2003) Chromosomal localization of 5S and 18S–5.8S–25S ribosomal DNA sites in five Asian pines using fluorescence in situ hybridization. Theor Appl Genet 106:198–204

    Article  CAS  PubMed  Google Scholar 

  48. Venora G, Blangiforti S, Frediani M, Maggini F, Gelati MT, Castiglione MR, Cremonini R (2000) Nuclear DNA contents, rDNAs, chromatin organization, and karyotype evolution in Vicia sect. faba. Protoplasma 213:118–125

    Article  CAS  Google Scholar 

  49. Sone T, Fujisawa M, Takenaka M, Nakagawa S, Yamaoka S, Sakaida M, Nishiyama R, Yamato KT, Ohmido N, Fukui K, Fukuzawa H, Ohyama K (1999) Bryophyte 5S rDNA was inserted into 45S rDNA repeat units after the divergence from higher land plants. Plant Mol Biol 41:679–685

    Article  CAS  PubMed  Google Scholar 

  50. Belyayev A, Paštová L, Fehrer J, Josefiová J, Chrtek J, Mráz P (2018) Mapping of Hieracium (Asteraceae) chromosomes with genus–specific satDNA elements derived from next–generation sequencing data. Plant Syst Evol 304:387–396

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by National Science Centre, Poland, project no. 2017/27/B/NZ8/01478 to B.K.

Author information

Authors and Affiliations

  1. Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland

    Gülru Yücel, Magdalena Senderowicz & Bożena Kolano

  2. Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye

    Gülru Yücel

Authors
  1. Gülru Yücel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Magdalena Senderowicz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bożena Kolano
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bożena Kolano .

Editor information

Editors and Affiliations

  1. Institute of Botany, TU Dresden, Dresden, Germany

    Tony Heitkam

  2. Botanical Institute of Barcelona, Barcelona, Spain

    Sònia Garcia

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Yücel, G., Senderowicz, M., Kolano, B. (2023). The Use of Ribosomal DNA for Comparative Cytogenetics. In: Heitkam, T., Garcia, S. (eds) Plant Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2672. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3226-0_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3226-0_17

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3225-3

  • Online ISBN: 978-1-0716-3226-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation