Molecular phylogeny based on its sequences of nrDNA of some species belonging to dodder (Cuscuta L.) genus from various ecological sites of Turkey

  • Ilhan KAYA Van Yuzuncu Yil University, Faculty of Agriculture, Department of Plant Protection, Van
  • Ibrahim DEMIR Bitlis Eren University, Faculty of Arts and Sciences, Department of Biology, Bitlis
  • Mustafa USTA Van Yuzuncu Yil University, Faculty of Agriculture, Department of Plant Protection, Van
  • Hikmet M. SIPAHIOĞLU Malatya Turgut Ozal University, Faculty of Agriculture, Department of Plant Protection, Malatya
Keywords: classification; Cuscuta spp.; molecular phylogeny; Turkey

Abstract

Nuclear ribosomal DNA (nrDNA) sequence data of the Cuscuta genus, which have been considered as one of the most popular sequences for phylogenetic inference in plants, have been studied from a phylogenetic perspective in agricultural and non-agricultural lands of Turkey. The samples of Cuscuta spp. were collected from different geographical regions of Turkey between the years of 2013-2015. Some other species, not available locally, were taken from the herbarium samples of some research units. In order to study the phylogenetic relations of collected species, DNA isolations were made from body tissue samples. Conserved regions on ribosomal DNA (rDNA) were amplified by universal primers via PCR method and cloned into a proper cloning vector. The cloned DNA fragments were sequenced and analysed by web-based and computer programs. DNA sequences of certain species were recorded to the National Center for Biotechnology Information (NCBI) database. Based on the morphological examination and molecular analyses of fresh and the herbarium specimen, 8 species were identified. The identified species were C. hyalina (Gene bank accession no. KY020420), C. monogyna (KY020421), C. europaea (KY020422), C. palaestina (KY020423), C. approximata (KY020424), C. kurdica (KY020427), C. kotschyana (KY020430) and C. babylonica (KY020431). The ITS (Internal Transcribed Spacer) region contains several indels in identified Cuscuta species with the length varying from 668 to 730 bp. Sequence divergence ranges from 1.00% to 8.00% within Cuscuta spp. Based on our findings, the ITS sequences provided phylogenetically informative results in combination with the secondary structures.

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References

Baldwin BG (1992). Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Molecular Phylogenetics and Evolution 1(1):3-16. https://doi.org/10.1016/1055-7903(92)90030-K

Baldwin BG, Sanderson MJ, Porter JM, Wojciechowoski MF, Campell CS, Donoghue MJ (1995). The ITS region of nuclear ribosomal DNA: Valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 2:250-272.

Benvenuti S, Dinelli G, Bonetti A, Catizone P (2005). Germination ecology, emergence and host detection in Cuscuta campestris. Weed Research 45:270-278. https://doi.org/10.1111/j.1365-3180.2005.00460.x

Chrtek J, Osbornova J (1991). Notes on the synanthropic plants of Egypt: 3. Grammica campestris and other species of family Cuscutaceae. Folia Geobotanica Phytotaxin 26:287-314. https://doi.org/10.1007/BF02912750

Costea M, Nesom GL, Stefanovic S (2006). Taxonomy of Cuscuta gronovii and Cuscuta umbrosa (Convolvulaceae). SIDA, Contributions to Botany 22:197-207.

Costea M, Tardif FJ (2006). The biology of Canadian weeds. Cuscuta campestris, C. gronovii, C. umbrosa, C. epithymum and C. epilinum. Canadian Journal of Plant Science 86:293-316. https://doi.org/10.4141/P04-077

Davis PH (1978). Flora of Turkey and the East Aegean Islands. Edinburgh University Press, Edinburgh.

Dawson JH, Musselman LJ, Wolswinkel P, Dorr I (1994). Biology and control of Cuscuta. Review of Weed Science 6:265-317. https://doi.org/10.3732/ajb.1300449

García MA, Costea M, Kuzmina M, Stefanović S (2014). Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences. American Journal of Botany 101 (4):670-690. https://doi.org/10.3732/ajb.1300449

Hadac E, Chrtek J (1970). Notes on the taxonomy of Cuscutaceae. Folia Geobotanica Phytotaxin 5:443-445.

Hutchison JM, Ashton FM (1979). Effect of desiccation and scarification on the permeability and structure of the seed coat of Cuscuta campestris. American Journal of Botany 66:40-46. https://doi.org/10.1002/j.1537-2197.1979.tb06191.x

Keskin F, Kaya I, Usta M, Demir I, Sipahioglu HM, Nemli Y (2017). Molecular cloning and sequence analysis of the its region of nuclear ribosomal DNA for species identification in dodders (Cuscuta; Convolvulaceae). International Journal of Agriculture and Biology 19(6):1447-1451. https://doi.org/10.17957/IJAB/15.0442

Kujit J (1969). The biology of parasitic flowering plants. University of California Press, Berkeley.

Li YH (1987). Parasitism and integrated control of dodder on soybean, in parasitic flowering plants. Weber HC, Forstreuter W (Eds). Marburg, Germany, pp 497-500.

Liao GI, Chen MY, Kuoh CS (2000). Cuscuta L. (Convolvulaceae) in Taiwan. Taiwania 45:226-234.

Mabberley DJ (1997). The plant-book: A portable dictionary of the vascular plants. Cambridge University Press, Cambridge, UK.

Mower JP, Stefanović S, Young GJ, Palmer JD (2004). Gene transfer from parasitic to host plants. Nature 432:165-166. https://doi.org/10.1038/432165b

Nemli Y, Kaya I, Tamer ŞR (2015). Cuscuta campestris. Turkey invasive plants catalog. Middle Black Sea Pass. Agricultural Research Station Directorate, Tokat.

Tippery NP, Les DH (2008). Phylogenetic analysis of the internal transcribed spacer (ITS) region in Menyanthaceae using predicted secondary structure. Molecular Phylogenetics and Evolution 49:526-537. https://doi.org/10.1016/j.ympev.2008.07.019

Parker C, Riches CR (1993). Parasitic weeds of the world. Biology and control. CAB International, Wallingford.

Podoplelova Y, Ryzhakov G (2005). Phylogenetic analysis of the order Nymphaeales based on the nucleotide sequences of the chloroplast ITS 2-4 region. Plant Science 169(3):606-611. https://doi.org/10.1016/j.plantsci.2005.05.006

Sambrook J, Fritsch EF, Maniatis T (1989). Molecular cloning: A laboratory manual, second edition, cold spring harbor laboratory press. Cold Spring Harbor, NY.

Soltis DE, Soltis PS, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, ... Sytsma KJ (1997). Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Annals of the Missouri Botanical Garden 84:1-49. https://doi.org/10.2307/2399952

Sonnate G, Glasso I, Pignone D (2003). ITS sequence analysis and phylogenetic inference in the genus Lens Mill. Annals of Botany 91:49-54. https://doi.org/10.1093/aob/mcg007

Stefanović S, Olmstead RG (2004). Testing the phylogenetic position of a parasitic plant (Cuscuta, Convolvulaceae, Asteridae): Bayesian inference and the parametric bootstrap on data drawn from three genomes. Systematic Biology 53 (3):384-399. https://doi.org/10.1080/10635150490445896

Stefanović S, Kuzmina M, Costea M (2007). Delimitation of major lineages within Cuscuta subgenus Grammica (dodder; Convolvulaceae) using plastid and nuclear DNA sequences. American Journal of Botany 94:568-589.

White TJ, Bruns T, Lee S, Taylor JW (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: A guide to methods and applications. (Innis MA, Gelfand DH, Sninsky JJ, White (Eds). Academic Press, New York, USA pp 315-322.

Yokoyama J, Suzuki M, Iwatsuki K, Hasebe M (2000). Molecular phylogeny of Coriaria, with special emphasis on the disjunct distribution. Molecular Phylogenetics and Evolution 14(1):11-19. https://doi.org/10.1006/mpev.1999.0672

Yunker TG (1932). The genus Cuscuta. Memoirs of the Torrey Botanical Club 18:113-331.

Published
2020-08-31
How to Cite
KAYA, I., DEMIR, I., USTA, M., & SIPAHIOĞLU, H. M. (2020). Molecular phylogeny based on its sequences of nrDNA of some species belonging to dodder (Cuscuta L.) genus from various ecological sites of Turkey. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 48(3), 1332-1340. https://doi.org/10.15835/nbha48311997
Section
Research Articles