The use of the intergenic spacer region psbA-trnH of the chloroplast genome for the analysis of the taxonomic position and genetic polymorphism of the Ukrainian populations of Tulipa quercetorum Klokov et Zoz

  • Y. O. Tynkevich Yuriy Fedkovych Chernivtsi National University Ukraine, 58012, Chernivtsi, Kotsyubynsky str. 2
  • I. I. Moysiyenko Kherson State University Ukraine, 73000, Kherson, University str. 27
  • R. A. Volkov Yuriy Fedkovych Chernivtsi National University Ukraine, 58012, Chernivtsi, Kotsyubynsky str. 2
DOI: https://doi.org/10.7124/visnyk.utgis.20.1-2.1508
Keywords: psbA-trnH, DNA-barcoding, Tulipa quercetorum, Tulipa sylvestris s. l.

Abstract

Aim. Tulipa quercetorum is included in the Red Data Book of Ukraine as a vulnerable species. The International Botanical Taxonomy considers T. quercetorum synonymous with T. sylvestris, a wide-ranging polymorphic species. The necessity and type of conservation measures aimed at preserving Ukrainian populations of T. quercetorum depend on its taxonomic interpretation. Accordingly, we used the chloroplast marker psbA-trnH to analyze the taxonomic status of the Ukrainian populations of T. quercetorum. Methods. PCR amplification, sequencing of the psbA-trnH spacer region, and bioinformatic analysis. Results. We have sequenced psbA-trnH of four accessions of T. quercetorum representing different regions of its distribution area in Ukraine. Comparison with the sequences of T. sylvestris s. l. showed that the differences in the psbA-trnH spacer are mainly represented by with oligonucleotide indels. Three out of four samples of T. quercetorum from Ukrainian populations contain a specific variant of inversion in the loop region of the 3' UTR of psbA mRNA, which is not characteristic for samples of T. sylvestris s. l. Conclusions. The data obtained indicate the genetic uniqueness of Ukrainian populations of T. quercetorum, however, for the accurate determination of its taxonomic status additional molecular markers, preferably of nuclear localization, are required.

References

Asgari D., Babaei A., Naghavi M. R., Kiani M. Biodiversity status of Tulipa (Liliaceae) in Iran inferred from molecular characterization. Hortic. Environ. Biotechnol. 2020. Vol. 61(3). P. 559-567. doi: 10.1007/s13580-019-00158-0

Christenhusz M. J., Govaerts R., David J. C., Hall T. et al. Tiptoe through the tulips–cultural history, molecular phylogenetics and classification of Tulipa (Liliaceae). Bot. J. Linn. Soc. 2013. Vol. 172(3). P. 280-328. doi: 10.1111/boj.12061

Darras A. Overview of the dynamic role of specialty cut flowers in the international cut flower market. Horticulturae. 2021. Vol. 7(3). P. 51. doi: 10.3390/horticulturae7030051

Didukh Y. P. Chervona knyha Ukrainy. Roslynnyi svit (Red Data Book of Ukraine. Plant Kingdom). 2009. Kyiv: Globalconsulting.

Do H. D. K., Kim C., Chase M. W., Kim J. H. Implications of plastome evolution in the true lilies (monocot order Liliales). Mol. Phylogenet. Evol. 2020. Vol. 148. e106818. doi: 10.1016/j.ympev.2020.106818

Grimm G. W., Schlee M., Komarova N. Y., Volkov R. A. et al. Low-level taxonomy and intrageneric evolutionary trends in higher plants. From plant taxonomy to evolutionary biology. Nova Acta Leopold. 2005. Vol. 92(342). P. 129-145.

Hajdari A., Pulaj B., Schmiderer C., Mala X., Wilson B. et al. A phylogenetic analysis of the wild Tulipa species (Liliaceae) of Kosovo based on plastid and nuclear DNA sequence. Adv. Genet. 2021. Vol. 2(3). e202100016. doi: 10.1002/ggn2.202100016

Idrees M., Wang H., Mitra L. P., Zhang Z. Y. et al. Phylogenetic study of Eriobotrya (Rosaceae) based on combined cpDNA psbA-trnH and atpB-rbcL markers. J. Trop. For. Sci. 2021. Vol. 33(3). P. 343-348. doi: 10.26525/jtfs2021.33.3.343

Jenks A. A., Walker J. B., Kim S. C. Phylogeny of New World Salvia subgenus Calosphace (Lamiaceae) based on cpDNA (psbA-trnH) and nrDNA (ITS) sequence data. J. Plant Res. 2013. Vol. 126(4). P. 483-496. doi: 10.1007/s10265-012-0543-1

Ju X., Shi G., Chen S., Dai W. et al. Characterization and phylogenetic analysis of the complete chloroplast genome of Tulipa patens (Liliaceae). Mitochondrial DNA Part B. 2021. Vol. 6(9). P. 2750-2751. doi: 10.1080/23802359.2021.1967799

Katoh K., Rozewicki J., Yamada K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings Bioinf. 2017. Vol. 20(4). P. 1160–1166. doi: 10.1093/bib/bbx108

Kelchner S. A., Group B. P. Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Mol. Phylogenet. Evol. 2013. Vol. 67(2). P. 404-413. doi: 10.1016/j.ympev.2013.02.005

Kowarik I., Wohlgemuth J. O. Tulipa sylvestris (Liliaceae) in northwestern Germany: a non-indigenous species as an indicator of previous horticulture. Polish Botanical Studies. 2006. Vol. 22. P. 317-331.

Li J., Price M., Su D. M., Zhang Z., et al. Phylogeny and comparative analysis for the plastid genomes of five Tulipa (Liliaceae). Biomed Res. Int. 2021. Vol. 2021. P. 1-10. doi: 10.1155/2021/6648429

Liu G., Lan Y., Qu L., Zhao Y. et al. Analyzing the genetic relationships in Tulipa based on karyotypes and 5S rDNA sequences. Sci. Hortic. 2022. Vol. 302. e111178 doi: 111178. 10.1016/j.scienta.2022.111178

Logacheva M. D., Valiejo-Roman C. M., Pimenov M. G. ITS phylogeny of West Asian Heracleum species and related taxa of Umbelliferae–Tordylieae WDJ Koch, with notes on evolution of their psbA-trnH sequences. Plant Syst. Evol. 2008. Vol. 270(3). P. 139-157. doi: 10.1007/s00606-007-0619-x

Marasek-Ciolakowska A., Ramanna M. S., Arens P., Van Tuyl J. M. Breeding and cytogenetics in the genus Tulipa. Floricult. Ornam. Biotechnol. 2012. Vol. 6. P. 90-97.

Miri S. M. Artificial polyploidy in the improvement of horticultural crops. J. Plant Physiol. Breed. 2020. Vol. 10(1). P. 1-28. doi: 10.22034/JPPB.2020.12490

Okonechnikov K., Golosova O., Fursov M., Ugene Team. Unipro UGENE: a unified bioinformatics toolkit. Bioinf. 2012. Vol. 28(8). P. 1166-1167. doi: 10.1093/bioinformatics/bts091

Panchuk I.I., Volkov R.A. A practical course in molecular genetics. Chernivtsi: Ruta. 2007. 120 p. [In Ukranian] / Панчук І.І. Волков Р.А. Практикум з молекулярної генетики. Чернівці: Рута. 2007. 120 с.

Pang X., Liu C., Shi L., Liu R., 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(11). e48833. doi: 10.1371/journal.pone.0048833

Peregrym M. M. Representation of bulb and bulbotuberiferous species of the natural flora of Ukraine in protected plant lists of different levels. Ukr. Botan. Journ. 2012. Vol. 69(6). P. 832-846 [In Ukranian]

Peterson A., John H., Koch E., Peterson J. A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences. Plant Syst. Evol. 2004. Vol. 245(3). P. 145-162. doi: 10.1007/s00606-003-0114-y

Porebski S., Bailey L. G., 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(1). P. 8-15. doi: 10.1007/BF02772108.

Pourkhaloee A., Khosh-Khui M., Arens P., Salehi H. et al. Molecular analysis of genetic diversity, population structure, and phylogeny of wild and cultivated tulips (Tulipa L.) by genic microsatellites. Hort. Environ. Biotech. 2018. Vol. 59(6) P. 875-888. doi: 10.1007/s13580-018-0055-6

Qu L., Xue L., Xing G., Zhang Y. et al. Karyotype analysis of eight wild Tulipa species native to China and the interspecific hybridization with tulip cultivars. Euphytica. 2018. Vol. 214(4). P. 1-12. doi: 10.1007/s10681-018-2151-1

Simeone M. C., Cardoni S., Piredda R., Imperatori F. et al. Comparative systematics and phylogeography of Quercus section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation. PeerJ. 2018. Vol. 6. e5793. doi: 10.7287/peerj.preprints.26995

Small R. L., Cronn R. C., Wendel J. F. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 2004. Vol. 17(2). P. 145-170. doi: 10.1071/SB03015

Smith S. A., Brown J. W. Constructing a broadly inclusive seed plant phylogeny. Am. J. Bot. 2018. Vol. 105(3). P. 302-314. doi: 10.1002/ajb2.1019

Stefanaki A., Walter T., van Andel T. Tracing the introduction history of the tulip that went wild (Tulipa sylvestris) in sixteenth-century Europe. Sci. Rep. 2022. Vol. 12(1). P. 1-18. doi: 10.1038/s41598-022-13378-9

Štorchová H., Olson M. S. The architecture of the chloroplast psbA-trnH non-coding region in angiosperms. Plant Syst. Evol. 2007. Vol. 268(1). P. 235-256.

Turktas M., Metin Ö. K., Baştuğ B., Ertuğrul F. et al. Molecular phylogenetic analysis of Tulipa (Liliaceae) based on noncoding plastid and nuclear DNA sequences with an emphasis on Turkey. Bot. J. Linn. Soc. 2013. Vol. 172(3). P. 270-279. doi: 10.1111/j.0024-4074.2004.00194.x

Tynkevich Y. O., Biliay D. V., Volkov R. A. Utility of the trnH–psbA region for DNA barcoding of Aconitum anthora L. and related taxa. Faktori eksperimental’noi evolucii organizmiv. 2022a. Vol. 31. P. 134–41. [In Ukranian] doi: 10.7124/feeo.v31.1500

Tynkevich Y. O., Derevenko T. O., Chorney I. I. Phylogenetic relationships of Ukrainian accessions of Lathyrus venetus (Mill.) Wohlf. and L. vernus (L.) Bernh. based on the analysis of the psbA-trnH region of the chloroplast genome. Biol. Syst. 2022b. Vol. 14(1), P. 135-140. [In Ukranian] doi: 10.31861/biosystems2022.01.039

Wang Y. B., Liu B. B., Nie Z. L., Chen H. F. et al. Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming. J. Syst. Evol. 2020. Vol. 58(5). P. 673-695. doi: 10.1111/jse.12588

WFO World Flora Online. 2022. Available from: http://www.worldfloraonline.org/ (accessed 27 November 2022)

Whitlock B. A., Hale A. M., Groff P. A. Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PloS one. 2010. Vol. 5(7). e11533. doi: 10.1371/journal.pone.0011533

Wilford R. Tulips: Species and hybrids for the gardener. 2006. Portland, OR: Timber Press, 212 pp.

Xing G., Qu L., Zhang W., Zhang Y. et al. Study on interspecific hybridization between tulip cultivars and wild species native to China. Euphytica 2020. Vol. 216(4). P. 1-17. doi: 10.1007/s10681-020-02594-x

Yuan L., Yan X., Chen X., Zhu X. The complete chloroplast genome of Tulipa gesneriana (Liliaceae) and its phylogenetic analysis. Mitochondrial DNA Part B. 2022. Vol. 7(7). P. 1255-1256. doi: 10.1080/23802359.2022.2093676

Zarrei M., Wilkin P., Fay M. F., Ingrouille M. J. et al. Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): implications of analyses of nuclear ribosomal and plastid DNA sequences for infrageneric classification. Ann. Bot. 2009. Vol. 104(1). P. 125-142. doi: 10.1093/aob/mcp103

Zhuang Y., Wang X., Li X., Hu J. et al. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nat. Plants. 2022. Vol. 8(3). P. 233-244. doi: 10.1038/s41477-022-01102-4