THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L.

Year 2023, , 71 - 76, 15.04.2023

Aykut Yılmaz

https://doi.org/10.23902/trkjnat.1252980

Abstract

This study was performed to determine the phylogenetic relationships in the genus Potentilla L. and to assess the importance of the trnL/trnF intergenic spacer (IGS) region. The selection of DNA barcoding region to provide for more effective, accurate and consistent results in the analysis is one of the most important points in success of the study. For this purpose, 71 Potentilla taxa were examined based on trnL/trnF IGS sequence data of chloroplast DNA acquired from the National Center for Biotechnology Information (NCBI) and a Maximum Parsimony (MP) dendrogram was drawn. The trnL/trnF IGS region has the convenient sequence length for barcoding region, and it is also proposed the use of this region which has highly variable and parsimony informative sites. When the probabilities of substitutions from one base to another base for trnL/trnF IGS region were examined, it was assigned that the rate of transitional substitutions with 57.13% is higher than the transversional substitutions. The MP dendrogram revealed that the studies taxa were placed in six groups as Fragarioides, Reptans, Anserina, Alba, Himalayan and Argentea. Phylogenetic relationships within the Argentea clade, represented by the highest species number in this study, were observed as quite confusing compared to other clades. In order to get the most accurate results, it is necessary to determine the regions giving the best results, and then to use these regions together with as many taxa as possible. In conclusion, the using of trnL/trnF IGS sequence information that have high variable sites and grouping ability for studies taxa is strongly recommended.

Keywords

MP dendrogram, DNA barcoding, Phylogenetic relationships

Thanks

The author would like to thank to NCBI for sequence information used in this study and the authors sharing the sequence information in NCBI.

References

• 1. Bean, A.R. 2015. Notes on Potentilla (Rosaceae) and related genera in Australia. Muelleria, 33: 75-83.
• 2. Dobeš, C. & Paule, J. 2010. A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): Implications for its geographic origin, phylogeography and generic circumscription. Molecular Phylogenetics and Evolution, 56: 156-175.
• 3. Eriksson, T., Donoghue, M.J. & Hibbs, M.S. 1998. Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Systematics and Evolution, 211: 155-179.
• 4. Eriksson, T., Hibbs, M.S., Yoder, A.D., Delwiche, C.F. & Donoghue, M.J. 2003. The phylogeny of Rosoideae (Rosaceae) based on sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the trnL/F region of chloroplast DNA. International Jornal of Plant Sciences, 164 (2): 197-211.
• 5. Feng, T., Moore, M.J., Sun, Y., Meng, A., Chu, H., Li, J. & Wang, H. 2015. A new species of Argentina (Rosaceae, Potentilleae) from Southeast Tibet, with reference to the taxonomic status of the genus. Plant Systematics and Evolution, 301: 911-921.
• 6. Feng, T., Moore, M.J., Yan, M.H., Sun, Y.X., Zhang, H.J., Meng, A.P., Li, X.D., Jian, S.G., Li, J.Q. & Wang, H.C. 2017. Phylogenetic study of the tribe Potentilleae (Rosaceae), with further insight into the disintegration of Sibbaldia. Journal of Systematics and Evolution, 55(3): 177-191.
• 7. Goswami, D.A. & Matfield, B. 1975. Cytogenetic studies in the genus Potentilla L. New Phytologist, 75: 135-146.
• 8. Ilnicki, T. & Jeremi, K. 2008. Chromosome numbers of Potentilla subsect. Collinae (Rosaceae) from Poland. Caryologia, 61(2): 170-175.
• 9. Kalkman, C. 2004. Potentilla. In: Kubitzki K, ed. Flowering plants - Dicotyledons: Celastrales, Oxalidales, Rosales, Cornales, Ericales. Berlin: Springer, 366 pp.
• 10. Lundberg, M., Töpel, M., Eriksen, B., Nylander, J.A.A. & Eriksson, T. 2009. Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification. Molecular Phylogenetics and Evolution, 51: 269-280.
• 11. Müntzing, A. 1931. Note on the cytology of some apomictic Potentilla-species. Hereditas, 15: 166-178.
• 12. Müntzing, A. 1958. Further studies on intraspecific polyploidy in Potentilla argentea (coll). Botaniska Notiser, 111(1): 209-227.
• 13. NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank
• 14. Paule, J., Scherbantin, A. & Dobeš, C. 2012. Implications of hybridisation and cytotypic differentiation in speciation assessed by AFLP and plastid haplotypes–a case study of Potentilla alpicola La Soie. BMC Evolutionary Biology, 12: 132.
• 15. Persson, N.L., Toresen, I., Andersen, H.L., Smedmark, J.E.E. & Eriksson, T. 2020a. Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers. Annals of Botany Plants, 12(3): plaa017.
• 16. Persson, N.L., Eriksson, T. & Smedmark, J.E.E. 2020b. Complex patterns of reticulate evolution in opportunistic weeds (Potentilla L., Rosaceae), as revealed by low-copy nuclear markers. BMC Evolutionary Biology, 20: 38.
• 17. Persson, N.L. 2021. The taxonomy and molecular phylogeny of Potentilla L. (Rosaceae)-An investigation of generic delimitation and reticulate evolution, using low-copy nuclear markers. Thesis for the degree of Philosophiae Doctor (PhD). University of Bergen, Norway.
• 18. Rice, A., Glick, L., Abadi, S., Einhorn, M., Kopelman, N.M., Salman-Minkov, A., Mayzel, J., Chay, O. & Mayrose, I. 2014. The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers. New Phytologist, 206(1): 19-26.
• 19. Rieseberg, L.H. & Ellstrand, N.C. 1993. What can molecular and morphological markers tell us about plant hybridization? Critical Reviews in Plant Sciences, 12: 213-241.
• 20. Skalinska, M. 1950. Studies in chromosome numbers of Polish Angiosperms. Acta Societatis Botanicorum Poloniae, 20(1): 45-68.
• 21. Soják, J. 2009. Potentilla (Rosaceae) in the former USSR; second part: comments. Notes on Potentilla XXIV. Feddes Repertorium, 120: 185-217.
• 22. Tamura, K., Stecher, G. & Kumar, S. 2021. MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7): 3022-3027.
• 23. Töpel, M., Lundberg, M., Eriksson, T. & Eriksen, B. 2011. Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae). PLoS Currents, 3: RRN1237.
• 24. Töpel, M., Antonelli, A., Yesson, C. & Eriksen, B. 2012. Past climate change and plant evolution in Western North America: A case study in Rosaceae. PLOS ONE, 7(12): e50358.
• 25. Wolf, T. 1908. Monographie der Gattung Potentilla. Stuttgart: Bibliotheca Botanica, 16: 1-714.
• 26. Xiang, Y., Huang, C.H., Hu, Y., Wen, J., Li, S., Yi, T., Chen, H., Xiang, J. & Ma, H. 2017. Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication. Molecular Biology and Evolution, 34: 262-281.
• 27. Zhang, S.D., Jin, J.J., Chen, S.Y., Chase, M.W., Soltis, D.E., Li, H.T., Yang, J.B. & Yi, T.S. 2017. Diversification of Rosaceae since the late Cretaceous based on plastid phylogenomics. New Phytologist, 214: 1355-1367.