Skip to main content
SpringerLink
Log in

Molecular Phylogeny and Genetic Diversity of Carpathian Members of the Genus Muscari Inferred from Plastid DNA Sequences

  • Published:
Cytology and Genetics Aims and scope Submit manuscript

Abstract

The genus Muscari Mill. (Asparagaceae Juss.) includes about 80 species distributed in Eurasia, mainly in the Mediterranean region. Recent molecular phylogenetic studies have shown that the taxa belonging to this group form a monophyletic clade and are closely related. However, the phylogeny and status of some taxa of Muscari sensu lato remain controversial. So far, most phylogenetic studies of the genus Muscari have used almost exclusively Mediterranean plant material, while representatives of the genus from the Carpathian region remain unexplored. In this work, we used the sequencing of three regions of chloroplast DNA, psbA-trnH, trnT-L, and trnL-F, to clarify the phylogenetic relationships in the genus Muscari, to assess the genetic polymorphism and taxonomic status of Ukrainian populations of M. botryoides, as well as specimens of other Muscari species from the Carpathian region. According to the results of the phylogenetic analysis, the genus Muscari is a monophyletic group that includes three subgenera: Muscari, Muscarimia, and Pseudomuscari. Leopoldia species have been placed in the subgenus Muscari. Specimens of M. botryoides from Ukraine and Austria together with M. transsilvanicum from Romania and M. serpentinicum/M. sandrasicum from Turkey form the clade “Botryoides”, one of the three main clades identified in the subgenus Muscari. A significant genetic distance between Ukrainian specimens of M. botryoides, specimens of this species from other habitats, and other species of the genus Muscari allows us to consider the Ukrainian specimens of M. botryoides as a new, previously undescribed species. A comparison of the sequences of the investigated regions of the chloroplast genome revealed genetic differences between two groups of Ukrainian populations of M. botryoides, which can be interpreted as the existence of two intraspecific forms.

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.
Fig. 4.
Fig. 5.

Similar content being viewed by others

REFERENCES

  1. Ali, S.S., Yu, Y., Pfosser, M., and Wetschnig, W., Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies), Ann. Bot., 2012, vol. 109, no. 1, pp. 95–107. https://doi.org/10.1093/aob/mcr274

    Article  PubMed  Google Scholar 

  2. Andrino, C.O., Sano, P.T., Inglis, P.W., Hensold, N., Costa, F.N., and Simon, M.F., Phylogenetics of Paepalanthus (Eriocaulaceae), a diverse Neotropical monocot lineage, Bot. J. Linn. Soc., 2021, vol. 195, no. 1, pp. 34–52. https://doi.org/10.1093/botlinnean/boaa070

    Article  Google Scholar 

  3. Anisimova, M. and Gascuel, O., Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative, Syst. Biol., 2006, vol. 55, pp. 539–552. https://doi.org/10.1080/10635150600755453

    Article  PubMed  Google Scholar 

  4. Böhnert, T., Neumann, M., Quandt, D., and Weigend, M., Phylogeny based generic reclassification of Muscari sensu lato (Asparagaceae) using plastid and genomic DNA, Taxon, 2023, vol. 72, no. 2, pp. 261–277. https://doi.org/10.1002/tax.12864

    Article  Google Scholar 

  5. Bojnanský, V. and Fargašová, A., Atlas of Seeds and Fruits of Central and East-European Flora: the Carpathian Mountains region, Springer Sci. Business Media, 2007. https://doi.org/10.17221/18/2008-pps

  6. Borzatti von Loewenstern, A., Giordani, T., Astuti, G., Andreucci, A., and Peruzzi, L., Phylogenetic relationships of Italian Bellevalia species (Asparagaceae), inferred from morphology, karyology and molecular systematics, Plant Biosyst., 2013, vol. 147, no. 3, pp. 776–787. https://doi.org/10.1080/11263504.2013.829884

    Article  Google Scholar 

  7. Boychuk, S.V. and Budzhak, V.V., Modern views on phylogeny and systematic position of the genus Muscari (Asparagaceae) Miller. Scientific Herald of Chernivtsi University, Biology, 2020, vol. 12, no. 2, pp. 312–318. https://doi.org/10.31861/biosystems2020.02.312

  8. Boychuk, S.V. and Budzhak V.V., Intraspecific taxonomy of Muscari botryoides s. l. (Asparagaceae s. l. / Hyacinthaceae s. str.): history of research and synonymy, Ukr. Bot. J., 2021, vol. 78, no. 6, pp. 407–413. https://doi.org/10.15407/ukrbotj78.06.407

    Article  Google Scholar 

  9. Burland, T.G., DNASTAR’s Lasergene sequence analysis software, Bioinf. Methods Protoc., 1999, pp. 71–91. https://doi.org/10.1385/1-59259-192-2:71

  10. Coissac, E., Hollingsworth, P.M., Lavergne, S., and Taberlet, P., From barcodes to genomes: extending the concept of DNA barcoding, Mol. Ecol., 2016, vol. 25, no. 7, pp. 1423–1428. https://doi.org/10.1111/mec.13549

    Article  CAS  PubMed  Google Scholar 

  11. Dashwood, M. and Mathew, B., Hyacinthaceae-little blue bulbs, in RHS Plant Trials and Awards. Bulletin Number 11, Wisley: R. Hortic. Soc., 2005.

  12. Didukh, Y., Chervona knyha Ukrainy. Roslynnyi svit (Red Book of Ukraine. Flora), Kyiv: Hlobalkonsaltynkh, 2009.

  13. Dizkirici, A., Yigit, O., Pinar, M., and Eroglu, H., Molecular phylogeny of Muscari (Asparagaceae) inferred from cpDNA sequences, Biologia, 2019, vol. 74, pp. 205–214. https://doi.org/10.2478/s11756-018-00164-0

    Article  CAS  Google Scholar 

  14. Grimm, G.W., Denk, T., and Hemleben, V., Evolutionary history and systematics of Acer section Acer—a case study of low-level phylogenetics, Plant Syst. Evol., 2007, vol. 267, pp. 215–253. https://doi.org/10.1007/s00606-007-0572-8

    Article  Google Scholar 

  15. Grundmann, M., Rumsey, F.J., Ansell, S.W., Russell, S.J., Darwin, S.C., et al., Phylogeny and taxonomy of the bluebell genus Hyacinthoides, Asparagaceae [Hyacinthaceae], Taxon, 2010, vol. 59, no. 1, pp. 68–82. https://doi.org/10.1002/tax.591008

    Article  Google Scholar 

  16. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol., 2010, vol. 59, no. 3, pp. 307–321. https://doi.org/10.1093/sysbio/syq010

    Article  CAS  PubMed  Google Scholar 

  17. Huelsenbeck, J.P. and Ronquist, F., MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, 2001, vol. 17, no. 8, pp. 754–755. https://doi.org/10.1093/bioinformatics/17.8.754

    Article  CAS  PubMed  Google Scholar 

  18. Ishchenko, O.O., Panchuk, I.I., Andreev, I.O., Kunakh, V.A., and Volkov, R.A., Molecular organization of 5S ribosomal DNÀ of Deschampsia antarctica, Cytol. Genet., 2018, vol. 52, no. 6.,pp. 416–421. https://doi.org/10.3103/S0095452718060105

    Article  Google Scholar 

  19. Ishchenko, O.O., Bednarska, I.O., and Panchuk, I.I., Application of 5S ribosomal DNA for molecular taxonomy of subtribe Loliinae (Poaceae), Cytol. Genet., 2021, vol. 55, pp. 10–18. https://doi.org/10.3103/S0095452721010096

    Article  Google Scholar 

  20. Jafari, A. and Maassoumi, A.A., Synopsis of Leopoldia, Muscari and Pseudomuscari (Hyacinthaceae) in Iran, with Leopoldia ghouschtchiensis sp. nova, Ann. Bot. Fenn., 2011, vol. 48, no. 5, pp. 396–400. https://doi.org/10.5735/085.048.0502

    Article  Google Scholar 

  21. Katoh, K., Rozewicki, J., and Yamada, K.D., MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Brief Bioinf., 2019, vol. 20, pp. 1160–1166. https://doi.org/10.1093/bib/bbx108

    Article  CAS  Google Scholar 

  22. Kish, R., Chromosome numbers of bulbous monocotyledons of the Transcarpathian flora (Ukraine), Thaiszia, 2016, vol. 26, no. 1, pp. 21–26.

    Google Scholar 

  23. Kricsfalusy, V.V., Critical-systematic analysis of ephemeroid geophytes (Amaryllidales, Liliales) in the East Carpatian flora, Sci. Bull. Uzhhorod. Univ., Ser. Biol., 1999, vol. 6, pp. 21–32.

    Google Scholar 

  24. Kumar, S., Stecher, G., Knyaz, C., and Tamura, K., MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, no. 635, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Marhold, K., Multivariate morphometrics and its application to monography at specific and infraspecific levels, in Monographic Plant Systematics: Fundamental Assessment of Plant Biodiversity, Ruggell: Gantner, 2011, vols. 73–99.

  26. Mehmood, F., Ubaid, Z., Shahzadi, I., Ahmed, I., Waheed, M.T., Poczai, P., and Mirza, B., Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica), PeerJ, 2020, vol. 8, p. e9552. https://doi.org/10.7717/peerj.9552

    Article  PubMed  PubMed Central  Google Scholar 

  27. Nath, S., Sarkar, S., Patil, S.D., Saha, P.S., Lekhak, M.M., et al. Cytogenetic diversity in Scilloideae (Asparagaceae): a comprehensive recollection and exploration of karyo-evolutionary trends, Bot. Rev., 2023, vol. 89, pp. 158–200. https://doi.org/10.1007/s12229-022-09279-1

    Article  Google Scholar 

  28. Okonechnikov, K., Golosova, O., and Fursov, M., Unipro UGENE: a unified bioinformatics toolkit, Bioinformatics, 2012, vol. 28, no. 8, pp. 1166–1167. https://doi.org/10.1093/bioinformatics/bts091

    Article  CAS  PubMed  Google Scholar 

  29. Oyundelger, K., Harpke, D., Herklotz, V., Troeva, E., and Zheng, Z., Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia, J. Evol. Biol., 2022, vol. 35, no. 1, pp. 64–80. https://doi.org/10.1111/jeb.13960/v2/review2

    Article  PubMed  Google Scholar 

  30. Özüdoğru, B., Uler, A.D., Hacıoğlu, T.B., and Yıldırım, H., Phylogeny, biogeography, and character evolution in the genus Scilla s.l. and its close relatives Chionodoxa, Gemicia, Puschkinia, and Prospero (Asparagaceae), Plant Syst. Evol., 2022, vol. 308, no. 6, p. 44. https://doi.org/10.1007/s00606-022-01835-x

    Article  Google Scholar 

  31. Pang, X., Liu, C., Shi, L., Liu, R., Liang, D., et al., Utility of the trnH–psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis, PloS One, 2012, vol. 7, no. 11, p. e48833. https://doi.org/10.1371/journal.pone.0048833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Peregrym, M.M., Representation of bulb and bulbotuberiferous species of the natural flora of Ukraine in protected plant lists of different levels, Ukr. Bot. J., 2012, vol. 69, no. 6, pp. 832–846.

    Google Scholar 

  33. Phosser, M. and Speta, F., Phylogenetics of Hyacinthaceae based on plastid DNA sequences, Ann. Mo. Bot. Gard., 1999, vol. 86, no. 4, pp. 852–875. https://doi.org/10.2307/2666172

    Article  Google Scholar 

  34. 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

    Article  CAS  Google Scholar 

  35. Saha, P.S. and Jha, S., A molecular phylogeny of the genus Drimia (Asparagaceae: Scilloideae: Urgineeae) in India inferred from non-coding chloroplast and nuclear ribosomal DNA sequences, Sci. Rep., 2019, vol. 9, p. 7563. https://doi.org/10.1038/s41598-019-43968-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Simeone, M.C., Cardoni, S., Piredda, R., Imperatori, F., Avishai, M., Grimm, G.W., and Denk, T., Comparative systematics and phylogeography of Quercus section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation, PeerJ, 2018, vol. 6, p. e5793. https://doi.org/10.7287/peerj.preprints.26995v1

    Article  PubMed  PubMed Central  Google Scholar 

  37. Somanathan, I. and Baysdorfer, C., A bioinformatics approach to identify telomere sequences, Biotechniques, 2018, vol. 65, no. 1, pp. 20–25. https://doi.org/10.2144/btn-2018-0057

    Article  CAS  PubMed  Google Scholar 

  38. Speta, F., Hyacinthaceae, in Flowering Plants Monocotyledons: Lilianae (except Orchidaceae), 1998, pp. 261–285. https://doi.org/10.1007/978-3-662-03533-7_35

  39. Štorchová, H. and Olson, M.S., The architecture of the chloroplast psbA-trnH non-coding region in angiosperms, Plant Syst. Evol., 2007, vol. 268, no. 1, pp. 235–256. https://doi.org/10.1007/s00606-007-0582-6

    Article  CAS  Google Scholar 

  40. Taberlet, P., Gielly, L., Pautou, G., and Bouvet, J., Universal primers for amplification of three non-coding regions of chloroplast DNA, Plant Mol. Biol., 1991, vol. 17, pp. 1105–1109. https://doi.org/10.1007/bf00037152

    Article  CAS  PubMed  Google Scholar 

  41. 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 

  42. Tynkevich, Y.O., Boychuk, S.V., and Chorney, I.I., Assessment of the possibility of using the chloroplast genome region psbA-trnH for the study of genetic polymorphism of Ukrainian populations of Muscari botryoides (L.) Mill. Scientific Herald of Chernivtsi University, Biology, 2022a, vol. 14, no. 2, pp. 124–128. https://doi.org/10.31861/biosystems2022.02.124

    Article  Google Scholar 

  43. Tynkevich, Y.O., Shelyfist, A.Y., Kozub, L.V., Hemleben, V., Panchuk, I.I., and Volkov, R.A., 5S ribosomal DNA of genus Solanum: molecular organization, evolution, and taxonomy, Front. Plant Sci., 2022b, vol. 13, no. 852406. https://doi.org/10.3389/fpls.2022.852406

    Article  PubMed  PubMed Central  Google Scholar 

  44. Vozárová, R., Herklotz, V., Kovařík, A., Tynkevich, Y.O., Volkov, R.A., Ritz, C.M., and Lunerová, J., Ancient origin of two 5S rDNA families dominating in the genus Rosa and their behavior in the Canina-type meiosis, Front. Plant Sci., 2021, vol. 12, no. 643548. https://doi.org/10.3389/fpls.2021.643548

    Article  PubMed  PubMed Central  Google Scholar 

  45. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., and Barton, G.J., Jalview Version 2—a multiple sequence alignment editor and analysis workbench, Bioinformatics, 2009, vol. 25, no. 9, pp. 1189–1191. https://doi.org/10.1093/bioinformatics/btp033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. WCSP World Checklist of selected plant families. Facilitated by the Royal Botanic Gardens, Kew, 2023. http://wcsp.science.kew.org/. Accessed March 7, 2023.

  47. WFO World Flora Online, 2023. http://www.worldfloraonline.org/. Accessed March 7, 2023.

Download references

Funding

The study was supported by the Ministry of Education and Science of Ukraine, grant no. 0122U001335.

Author information

Authors and Affiliations

  1. Yuriy Fedkovych Chernivtsi National University, 58012, Chernivtsi, Ukraine

    Y. O. Tynkevich, S. V. Boychuk, A. Y. Shelyfist, I. I. Chorney & R. A. Volkov

Authors
  1. Y. O. Tynkevich
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. V. Boychuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. Y. Shelyfist
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. I. I. Chorney
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. R. A. Volkov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. A. Volkov.

Ethics declarations

The authors declare that they have no conflicts of interest. This study does not contain any investigations involving humans and vertebral animals as study objects.

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tynkevich, Y.O., Boychuk, S.V., Shelyfist, A.Y. et al. Molecular Phylogeny and Genetic Diversity of Carpathian Members of the Genus Muscari Inferred from Plastid DNA Sequences. Cytol. Genet. 57, 387–398 (2023). https://doi.org/10.3103/S0095452723050079

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.3103/S0095452723050079

Keywords:

Search

Navigation