Evaluation of intragenomic polymorphism of ribosomal DNA ITS1 region in Taraxacum (Asteraceae: Crepidinae) by targeted NGS sequencing
UDCc 582.998.4+575.174.015.3(470)
Keywords:
apomixis, DNA homogenization, DNA phylogenetics, reticulate evolution, ribosomal DNA, Taraxacum
Abstract
The picture of intragenomic polymorphism of ITS1 region of rDNA repeats revealed by targeted high-throughput sequencing is a modern and simple method useful for phylogenetic purposes, and it can shed light on recent hybridizations. However, up to the present time it was not applied in Taraxacum, a taxonomically intricate genus with largely reticulate evolutionary pattern. We tested this approach on an exploratory set composed of 20 samples (8 species from 4 sections, including 5 species from the largest section Taraxacum), which were situated in different evolutionary and geographic distances from each other. Our results have shown that intragenomic polymorphism of ITS1 region of rDNA in Taraxacum may be successfully used for phylogenetic reconstructions. Species belonging to different sections were strikingly different by intragenomic polymorphism of rDNA, and substantial variability was also observed between some (but not all) specimens of section Taraxacum, giving preliminary evidence that this group may be not monomorphic. In the same time, 8 of 13 studied specimens from the section Taraxacum had ITS1 region substantially homogenized (dominant variant was at least 7 times more frequent than any other), which is considered connected with the age of the last hybridization event in corresponding lineages. Possibly, microspecies with substantially homogenized rDNA represent more strongly stabilized taxonomic units.
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Sennikov A. N. 2007. The genus Taraxacum (Asteraceae) in the Russian part of East Fennoscandia: distribution, new records and comparison of taxonomic concepts. Memoranda Soc. Fauna Fl. Fenn. 83: 59–81.
Trávníček B., Kirschner J., Štěpánek J., Vašut R. J. 2010. Taraxacum Wiggers – pampeliška (smetánka). In: Květena České republiky. Vol. 8. Prague: Academia. Pp. 23–269. [In Czech].
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Uhlemann I. 2003. Die Gattung Taraxacum (Asteraceae) im östlichen Deutschland. Mitt. Florist. Kart. Sachsen-Anhalt, Sonderheft: 1–136.
Uhlemann I., Kirschner J., Štěpánek J. 2016. Taraxacum. In: Rothmaler – Exkursionsflora von Deutschland. Gefäßpflanzen: Kritischer Ergänzungsband. Aufl. 11. Berlin, Heidelberg: Springer. Pp. 133–184.
Uhlemann I., Ritz C. M., Peñailillo P. 2009. Relationships in Taraxacum section Arctica s. l. (Asteraceae, Cichorieae) and allies based on nrITS. Feddes Repertorium 120(1–2): 35–47. DOI: 10.1002/fedr.200811193
Wang W., Zhang X., Garcia S., Leitch A. R., Kovařík A. 2023. Intragenomic rDNA variation – the product of concerted evolution, mutation, or something in between? Heredity 131: 179–188. DOI: 10.1038/s41437-023-00634-5
White T. J., Bruns T. D., Lee S. B., Taylor J. W. 1990. Amplification and direct sequencing of fungal ribosomal RNA Genes for phylogenetics. In: M. A. Innis, D. H. Gelfand, J. J. Sninsky, T. J. White (eds.). PCR Protocols: A Guide to Methods and Applications. New York: Academic Press. Pp. 315–322. DOI: 10.1016/B978-0-12-372180-8.50042-1
Wolanin M., Klichowska E., Jedrzejczyk I., Rewers M., Nobis M. 2023. Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland. PhytoKeys 224: 1–88. DOI: 10.3897/phytokeys.224.99463
Záveská Drábková L., Kirschner J., Štěpánek J., Záveský L., Vlček Č. 2009. Analysis of nrDNA polymorphism in closely related diploid sexual, tetraploid sexual and polyploid agamospermous species. Plant Syst. Evol. 278: 67–85. DOI: 10.1007/s00606-008-0134-8
Clement M., Posada D., Crandall K. A. 2000. TCS: A computer program to estimate gene genealogies. Mol. Ecol. 9: 1657–1660.
Doyle J. J., Doyle J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11–15.
Edgar R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461. DOI: 10.1093/bioinformatics/btq461.
Katoh K., Standley D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30(4): 772–780. DOI: 10.1093/molbev/mst010
Kirschner J., Oplaat C., Verhoeven K. J. F., Zeisek V., Uhlemann I., Trávníček B., Räsänen J., Wilschut R. A., Štěpánek J. 2016. Identification of oligoclonal agamospermous microspecies: taxonomic specialists versus microsatellites. Preslia 88(1): 1–17.
Kirschner J., Štěpánek J., Klimeš L., Dvorský M., Brůna J., Macek M., Kopecký M. 2020. The Taraxacum Flora of Ladakh, with notes on the adjacent regions of the West Himalaya. Phytotaxa 457(1): 1–409. DOI: 10.11646/phytotaxa.457.1.1
Kirschner J., Štěpánek J., Mes T. H. M., den Nijs J. C. M., Oosterveld P., Štorchová H., Kuperus P. 2003. Principal features of the cpDNA evolution in Taraxacum (Asteraceae, Lactuceae): a conflict with taxonomy. Plant Syst. Evol. 239: 231–255. DOI: 10.1007/s00606-003-0002-5
Kirschner J., Záveská Drábková L., Štěpánek J., Uhlemann I. 2015. Towards a better understanding of the Taraxacum evolution (Compositae – Cichorieae) on the basis of nrDNA of sexually reproducing species. Plant Syst. Evol. 301: 1135–1156. DOI: 10.1007/s00606-014-1139-0
Kumar S., Stecher G., Li M., Knyaz C., Tamura K. 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547–1549. DOI: 10.1093/molbev/msy096
Letunic I., Bork P. 2021. Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucl. Acids Res. 49: W293–W296. DOI: 10.1093/nar/gkab301
Lundevall C. F., Øllgaard H. 1999. The genus Taraxacum in the Nordic and Baltic countries: types of all specific, subspecific and varietal taxa, including type locations and sectional belonging. Preslia 71(1–2): 43–171.
Machackova P., Majeský L., Hrones M., Bilkova L., Hribova E., Vasut R. J. 2022. New insights into ribosomal DNA variation in apomictic and sexual Taraxacum (Asteraceae). Bot. J. Linn. Soc. 199(4): 790-815.
Majeský L., Vašut R. J., Kitner M. 2015. Genotypic diversity of apomictic microspecies of the Taraxacum scanicum group (Taraxacum sect. Erythrosperma). Plant Syst. Evol. 301: 2105–2124. DOI: 10.1007/s00606-015-1218-x
Mes T. H. M., Kuperus P., Kirschner J., Štěpánek J., Štorchová H., Oosterveld P., den Nijs J. C. M. 2002. Detection of genetically divergent clone mates in apomictic dandelions. Molec. Ecol. 11: 253–265.
Múrias dos Santos A., Cabezas M. P., Tavares A. I., Xavier R., Branco M. 2016. tcsBU: A tool to extend TCS network layout and visualization. Bioinformatics 32: 627–628.
Nelson J. O., Watase G. J., Warsinger-Pepe N., Yamashita Y. M. 2019. Mechanisms of rDNA copy number maintenance. Trends Genet. 35(10): 734–742. DOI: 10.1016/j.tig.2019.07.006
Nguyen L.-T., Schmidt H. A., von Haeseler A., Minh B. Q. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32: 268–274. DOI: 10.1093/molbev/msu300
Øllgaard H. 1983. Hamata, a new section of Taraxacum (Asteraceae). Plant Syst. Evol. 141: 199–217.
Richards A. J. 1985. Sectional nomenclature in Taraxacum (Asteraceae). Taxon 34: 633–644.
Richards A. J. 2021. Field Handbook to British and Irish Dandelions. B.S.B.I. Handbook no. 23. Durham: Botanical Society of Britain and Ireland. 302 pp.
Rideout J. R., Caporaso G., Bolyen E., McDonald D., Vázquez Baeza Y., Alastuey J. C., et al. 2023. Biocore/scikit-bio: scikit-bio 0.5.9: Maintenance release. URL: https://zenodo.org/records/8209901 (Accessed 25 March 2024).
Ridgway K. P., Duck J. M., Young J. P. 2003. Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron. BMC Ecol. 3: 8. DOI: 10.1186/1472-6785-3-8
Salih R. H. M., Majeský L., Schwarzacher T., Gornall R. Heslop-Harrison P. 2017. Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies. PLoS ONE 12(2): e0168008. DOI: 10.1371/journal.pone.0168008
Sennikov A. N. 2007. The genus Taraxacum (Asteraceae) in the Russian part of East Fennoscandia: distribution, new records and comparison of taxonomic concepts. Memoranda Soc. Fauna Fl. Fenn. 83: 59–81.
Trávníček B., Kirschner J., Štěpánek J., Vašut R. J. 2010. Taraxacum Wiggers – pampeliška (smetánka). In: Květena České republiky. Vol. 8. Prague: Academia. Pp. 23–269. [In Czech].
Цвелёв Н. Н. Taraxacum Wigg. // Флора европейской части СССР. Т. 8. Л.: Наука, 1989. С. 61–114.
Uhlemann I. 2003. Die Gattung Taraxacum (Asteraceae) im östlichen Deutschland. Mitt. Florist. Kart. Sachsen-Anhalt, Sonderheft: 1–136.
Uhlemann I., Kirschner J., Štěpánek J. 2016. Taraxacum. In: Rothmaler – Exkursionsflora von Deutschland. Gefäßpflanzen: Kritischer Ergänzungsband. Aufl. 11. Berlin, Heidelberg: Springer. Pp. 133–184.
Uhlemann I., Ritz C. M., Peñailillo P. 2009. Relationships in Taraxacum section Arctica s. l. (Asteraceae, Cichorieae) and allies based on nrITS. Feddes Repertorium 120(1–2): 35–47. DOI: 10.1002/fedr.200811193
Wang W., Zhang X., Garcia S., Leitch A. R., Kovařík A. 2023. Intragenomic rDNA variation – the product of concerted evolution, mutation, or something in between? Heredity 131: 179–188. DOI: 10.1038/s41437-023-00634-5
White T. J., Bruns T. D., Lee S. B., Taylor J. W. 1990. Amplification and direct sequencing of fungal ribosomal RNA Genes for phylogenetics. In: M. A. Innis, D. H. Gelfand, J. J. Sninsky, T. J. White (eds.). PCR Protocols: A Guide to Methods and Applications. New York: Academic Press. Pp. 315–322. DOI: 10.1016/B978-0-12-372180-8.50042-1
Wolanin M., Klichowska E., Jedrzejczyk I., Rewers M., Nobis M. 2023. Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland. PhytoKeys 224: 1–88. DOI: 10.3897/phytokeys.224.99463
Záveská Drábková L., Kirschner J., Štěpánek J., Záveský L., Vlček Č. 2009. Analysis of nrDNA polymorphism in closely related diploid sexual, tetraploid sexual and polyploid agamospermous species. Plant Syst. Evol. 278: 67–85. DOI: 10.1007/s00606-008-0134-8
Published
2024-11-10
How to Cite
Efimov P. G., Domashkina V. V., Machs E. M., Zhurbenko P. M. Evaluation of intragenomic polymorphism of ribosomal DNA ITS1 region in Taraxacum (Asteraceae: Crepidinae) by targeted NGS sequencing // Turczaninowia, 2024. Vol. 27, № 3. P. 97-109 DOI: 10.14258/turczaninowia.27.3.10. URL: http://turczaninowia.asu.ru/article/view/16097.
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