Genome wide analysis of 5s ribosomal RNA genes in Gentiana macrophylla

DOI: https://doi.org/10.7124/FEEO.v36.1709
Keywords: Gentiana macrophylla Pall., intergenic spacer, 5S rDNA, molecular organization, variation

Abstract

Due to their unique structure, 5S rRNA genes are used in research of genome evolution and as a molecular marker. Aim. The aim of the study was to investigate the intergenic spacer (IGS) of 5S rRNA genes of Gentiana macrophylla Pall. Methods. The bioinformatic analysis of nucleotide sequences of 5S rDNA IGS found by searching the reference G. macrophylla genome was conducted. Results. It was determined that the majority of 5S rRNA genes in the G. macrophylla genome (approximately 460 copies) are arranged as tandem repeats on chromosome 7. The IGS region was found to be variable in terms of length and sequence, and all repeats were divided into four classes. Of these, 84% were similar in their nucleotide sequence to 5S rDNA IGS of two other species of the Cruciata section. The IGS of all classes contains regulatory elements typical for 5S rDNA of other flowering plants. The differences among the various classes are attributable to the presence of duplicated regions at the beginning of the IGS. This mechanism of IGS evolution due to the duplication at the beginning of the spacer has been previously identified in other gentians. Conclusions. The data obtained indicate the existence of different variants of 5S rDNA repeats in the G. macrophylla genome, which may provide the basis for genetic plasticity.

References

POWO. Gentiana macrophylla [Internet]. Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet. 2025. Available from: https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:368470-1.

Yuan Y. M. Karyological studies on Gentiana section Cruciata Gaudin (Gentianaceae) from China. Caryologia. 1993. Vol. 46 (2–3). P. 99–114. doi: 10.1080/00087114.1993.10797252.

Tan R. X., Wolfender J. L., Zhang L. X., Ma W. G., Fuzzati N., Marston A., et al. Acyl secoiridoids and antifungal constituents from Gentiana macrophylla. Phytochemistry. 1996. Vol. 42 (5). P. 1305–1313. doi: 10.1016/0031-9422(96)00149-5.

Yu F., Yu F., Li R., Wang R. Inhibitory effects of the Gentiana macrophylla (Gentianaceae) extract on rheumatoid arthritis of rats. J. Ethnopharmacol. 2004. Vol. 95 (1). P. 77–81. doi: 10.1016/j.jep.2004.06.025.

Kim K., Rhee H., Park E., Jung K., Jeon H., Kim J.H., et al. Anti-inflammatory effects of Radix Gentianae Macrophyllae (Qinjiao), Rhizoma Coptidis (Huanglian) and Citri Unshiu Pericarpium (Wenzhou migan) in animal models. Chin. Med. 2008. Vol. 3 (1). P. 10. doi: 10.1186/1749-8546-3-10.

Zhou T., Bai G., Hu Y., Ruhsam M., Yang Y., Zhao Y. De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. DNA Res. 2022. Vol. 29 (6). doi: 10.1093/dnares/dsac034.

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

Andreev I. O., Melnyk V. M., Myryuta G. Y., Kunakh V. A. Polymorphism of 5S rDNA intergenic spacer in some Gentiana species. Factors Exp. Evol. Org. 2017. Vol. 20. P. 42–6. doi: 10.7124/FEEO.v20.731.

Andreev I. O., Melnyk V. M., Miryuta G. Y., Shelifist A. E., Volkov R. A., Kunakh V. A. Molecular organization of the intergenic spacer of 5S rDNA in some species of the genus Gentiana L. In: Volkov R, editor. 5S ribosomal DNA of flowering plants [Internet]. Chernivtsi: Yuriy Fedkovych Chernivtsi National University. 2021. P. 105–122. Available from: http://utgis.org.ua/images/pdf/books/Volkov_Monograph.pdf.

Mel’nyk V. M., Andreev I. O., Myryuta G. Y., Shelyfist A. Y., Volkov R. A., Kunakh V. A. Molecular organization of 5S rDNA intergenic spacer in Gentiana pneumonanthe L. and G. punctata L. Bull. Vavilov Soc. Genet. Breeders Ukr. 2020. Vol. 18 (1–2). P. 9–15. doi: 10.7124/visnyk.utgis.18.1-2.1349.

Mel’nyk V. M., Andreev I. O., Volkov R. A., Kunakh V. A. 5S rDNA intergenic spacer of some species of Cruciata and Chondrophyllae sections and its application in taxonomy of genus Gentiana. Fakt. Eksp. Evol. Org. 2024. Vol. 34. P. 75–81. doi: 10.7124/FEEO.v34.1620.

Okonechnikov K., Golosova O., Fursov M., Varlamov A., Vaskin Y., Efremov I., et al. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics. 2012. Vol. 28 (8). P. 1166–1167. doi: 10.1093/BIOINFORMATICS/BTS091.

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

Tomiczak K. Molecular and cytogenetic description of somatic hybrids between Gentiana cruciata L. and G. tibetica King. J. Appl. Genet. 2020. Vol. 61 (1). P. 13–24. doi: 10.1007/s13353-019-00530-x.