Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences

  • Emre SEVINDIK Adnan Menderes University, Faculty of Agriculture, Department of Agricultural Biotechnology, South Campus, Cakmar, Aydin (TR) https://orcid.org/0000-0002-2423-5176
  • Melike AYDOGAN Adnan Menderes University, Faculty of Agriculture, Department of Agricultural Biotechnology, South Campus, Cakmar, Aydin (TR)
  • Mehmet Y. PAKSOY Munzur University, Tunceli Vocational School, Department of Medical Services and Techniques, Medical Documentation and Secretaryship Pr. Tunceli (TR)
Keywords: Conringia, phylogenetic analysis, nrITS, trnL-F, Turkey

Abstract

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

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References

Ahmed NU, Park JI Kim HR, Nou IS Nou (2012). Progress in genetic manipulation of the Brassicaceae. Journal of Plant Biotechnology 39(1):1-12. http://dx.doi.org/10.5010/JPB.2012.39.1.001

Al-Shehbaz IA, Mutlu, B, Dönmez AA 2007. The Brassicaceae (Cruciferae) of Turkey, updated. Turkish Journal of Botany 31(4):327-336.

Bulbul AS, Kader Varlik MA, Arslan A (2019). Fruits, seeds and pollen morphology of Alyssum L. (Brassicaceae) and their taxonomic value. Fresenius Environmental Bulletin 28(3):2199-2219.

Bulbul AS, Varlik K, Armagan M (2018). Taxonomic implication of trichomes on silicules in Alyssum L. (Brassicaceae) species in Turkey. Fresenius Environmental Bulletin 27(12B): 9581-9589.

Couvreur TL, Franzke A, Al-Shehbaz A., Bakker FT, Koch MA, Mummenhoff K (2010). Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Molecular Biology and Evolution 27(1):55-71. https://doi.org/10.1093/molbev/msp202

Demir I, Kaya İ, Usta M, Sipahioğlu HM (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

Dönmez AA, Aydın ZU, Wang X (2021). Wild Brassica and its close relatives in Turkey, the genetic treasures. Horticultural Plant Journal 7(2):97-107. https://doi.org/10.1016/j.hpj.2020.11.003

Drabkova L, Kirschner J, Vlček Č, Pačes V (2004). TrnL–trnF intergenic spacer and trnL intron define major clades within Luzula and Juncus (Juncaceae): importance of structural mutations. Journal of Molecular Evolution 59(1):1-10. https://doi.org/10.1007/s00239-004-2598-7

Felsenstein J (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.

Filiz E, Uras ME, Ozyigit II, Sen U, Gungor H (2018). Genetic diversity and phylogenetic analyses of Turkish rice varieties revealed by ISSR markers and chloroplast trnl-F region. Fresenius Environmental Bulletin 27(12):8351-8358.

Gidik B, Gül V, Sefali A (2019). A study of wild plant species of Brassicaceae family in Bayburt region of Turkey. Pakistan Journal of Botany 51(2):681-687.

Guo GY, Chen F, Shi XD, Tian YS, Yu M Q, Han XQ, ... Zhang Y (2016). Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences. Comptes Rendus Biologies 339(9-10):337-346. https://doi.org/10.1016/j.crvi.2016.06.004

Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analyses program for Windows 95/98/NT. Nucleic Acids Symposium 41:95-98.

Hedge IC (1965). Conringia adans. In: Davis PH (Ed). Flora of Turkey and the East Aegean Island, Vol 1, 275-279, Edinburgh University Press. Edinburgh.

Kaya E, Vatansever R, Filiz E (2018). Assessment of the genetic relationship of Turkish olives (Olea europaea subsp. europaea) cultivars based on cpDNA trnL-F regions. Acta Botanica Croatica 77(1):88-92. https://doi.org/10.1515/botcro-2017-0019

Kawarty AMA., Behçet L, Çakilcioğlu U (2020). An ethnobotanical survey of medicinal plants in Ballakayati (Erbil, North Iraq). Turkish Journal of Botany 44(3):345-357. https://doi.org/10.3906/bot-1910-39

Khan G, Zhang FQ, Gao QB, Fu PC, Xing R, Wang JL, ... Chen SL (2016). Phylogenetic reconstruction between the old and new world spiroides inferred from plastid trnL-F and nrDNA its sequences. Pakistan Journal of Botany 48(6):2399-2407.

Khosravi A R, Mohsenzadeh S, Mummenhoff K (2009). Phylogenetic relationships of Old World Brassicaceae from Iran based on nuclear ribosomal DNA sequences. Biochemical Systematics and Ecology 37(2):106-115. https://doi.org/10.1016/j.bse.2009.01.010

Koch M, Haubold B, Mitchell‐Olds T (2001). Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences. American Journal of Botany 88(3):534-544. https://doi.org/10.2307/2657117

Koch MA, Dobeš C, Kiefer C, Schmickl R, Klimeš L, Lysak MA (2007). Super network identifies multiple events of plastid trnF (GAA) pseudogene evolution in the Brassicaceae. Molecular Biology and Evolution 24(1):63-73. https://doi.org/10.1093/molbev/msl130

Liu L, Zhao B, Tan D, Wang J (2012). Phylogenetic relationships of Brassicaceae species based on matK sequences. Pakistan Journal of Botany 44(2):619-626.

Najarian F, Sheidai M, Koohdar F, Talebi SM (2020). Molecular phylogeny of the sect. Adonıs (Genus Adonis L., Ranunculaceae). Genetika. 52(3):1075-1086. https://doi.org/10.2298/GENSR2003075N

Özüdoğru B, Al-Shehbaz IA, Mummenhoff K (2017). Tribal assignment of Heldreichia Boiss. (Brassicaceae): evidence from nuclear ITS and plastidic ndhF markers. Plant Systematics and Evolution 303(3):329-335. https://doi.org/10.1007/s00606-016-1374-7

Penjor T, Anai T, Nagano Y, Matsumoto R, Yamamoto M (2010). Phylogenetic relationships of Citrus and its relatives based on rbcL gene sequences. Tree Genetics & Genomes 6(6):931-939. https://doi.org/10.1007/s11295-010-0302-1

Polat R, Güner B, Yüce Babacan E, Çakılcıoğlu U (2017). Survey of wild food plants for human consumption in Bingöl (Turkey). Indian Journal of Traditional Knowledge 16(3):378-384.

Poyraz I (2016). Comparison of ITS, RAPD, and ISSR from DNA-based genetic diversity techniques. Comptes Rendus Biologies 339(5-6):171-178. https://doi.org/10.1016/j.crvi.2016.04.001

Saitou N, Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Phylogenetic and Evolution 4(4):406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

Selvi S, Aladi HI, Paksoy MY (2019). Micromorphological and anatomical investigations on Conringia Heist. Ex Fabr. Bangladesh Journal of Botany 48(4):1153-1162. https://doi.org/10.3329/bjb.v48i4.49071

Sevindik E, Paksoy YM, Aydoğan M, Topseçer F (2020). Genetic variation and molecular relationships taxa of Conringia heist. ex Fabr (Brassicaceae) based on RAPD markers in Turkey. Genetika 52(1):107-114. https://doi.org/10.2298/GENSR2001107S

Sirali R, Uğur A, Zambi O, Dikmen A Çağlar S (2013). The importance of some species of Cruciferous (Brassicaceae) family for beekeeping Academic Journal of Agriculture 2(2):107-115.

Sun YL, Lee HB, Kim NY, Park WG, Hong SK (2012). Genetic diversity of Kalopanax pictus populations in Korea based on the nrDNA ITS sequence. Journal of Plant Biotechnology 39(1):75-80. http://dx.doi.org/10.5010/JPB.2012.39.1.075

Taberlet PT, Gielly L, Pautou G, Bouvet J (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17:1105-1109. https://doi.org/10.1007/BF00037152

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30(12): 2725-2729. https://doi.org/10.1093/molbev/mst197

Türktaş M, Aslay M, Kaya E, Ertuğrul F (2012). Molecular characterization of phylogenetic relationships in Fritillaria species inferred from chloroplast trnL-trnF sequences. Turkish Journal of Biology 36(5):552-560. https://doi.org/10.3906/biy-1201-30

Warwick SI, Sauder CA (2005). Phylogeny of tribe Brassiceae (Brassicaceae) based on chloroplast restriction site polymorphisms and nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences. Canadian Journal of Botany 83(5):467-483. https://doi.org/10.1139/b05-021

White TJ, Bruns T, Lee S, Taylor J (1990). Amplifications and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications. Innis M, Gelfand D, Sninsky J, White T (Ed). Academic Press, San Diego, California, USA, pp315-322.

Yilmaz-Çitak B, Dural H (2020). Fruit and seed micromorphology of the genus Iberis L. (Brassicaceae) in Turkey and its utility in taxonomic delimitation. Botanical Sciences 98(4):584-592. https://doi.org/10.17129/botsci.2573

Zhao B, Liu L, Tan D, Wang J (2010). Analysis of phylogenetic relationships of Brassicaceae species based on Chs sequences. Biochemical Systematics and Ecology 38(4):731-739. https://doi.org/10.1016/j.bse.2010.06.003

Published
2021-09-07
How to Cite
SEVINDIK, E., AYDOGAN, M., & PAKSOY, M. Y. (2021). Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences. Notulae Scientia Biologicae, 13(3), 11034. https://doi.org/10.15835/nsb13311034
Section
Research articles
CITATION
DOI: 10.15835/nsb13311034