Molecular Phylogenetic Analyses of Vicia L. (Fabaceae) Taxa Growing in the Southeastern Anatolia Region Based on Chloroplast TrnL Sequences

Year 2021, Volume: 5 Issue: 1, 11 - 22, 01.06.2021

Alevcan Kaplan , Alaattin Selçuk Ertekin Esra Gündüzer

https://doi.org/10.47947/ijnls.840322

Cited By: 1

Abstract

In the current study, some natural Vicia L. taxa growing naturally in the Southeast Anatolia Region were investigated from the point of view of molecular phylogenetic. For this purpose, transfer ribonucleic acid Leucine (trnL) was sequenced in order to study the phylogenetic relationships of the Vicia L. species. Lathyrus inconspicuous L. var. inconspicuous and Lathyrus cassius Boiss. were used as an outgroup. The length of the trnL area was determined approximately as 269-534 bp. The trnL sequences were submitted to the NCBI database and accession numbers received. We obtained information about the point mutations, as well as the protected and the changing characters. The taxa distinguished in the section level were separated and also grouped in terms of proximity on the phylogenetic tree (sect. Narbonensis, sect. Lathyroides, sect. Peregrinae, sect. Vicia, sect. Lentopsis). While, sect. Hypechusa, sect. Ervilia and sect. Cracca were not detailed to a great level of informativity. The data acquired were observed to be greatly reliable in terms of their ability to be used in solving taxonomical problems of the Vicia L. taxa.

Keywords

Fabaceae, Vicia L., Molecular phylogeny, cpDNA, sequencing

References

• Başbağ, M., Hoşgören, H., & Aydın, A. (2013). Vicia Taxa in the Flora of Turkey. Anadolu Tarım Bilimleri Dergisi, 28(1), 59-66.
• Binzat, O. K. (2012). Revision of Vicia L. (Leguminosae) in Central Anatolia, Turkey. Ph.D. Thesis, Middle East Technical University, Institute of Natural and Applied Sciences, September, Ankara.
• Bryant, J. A., & Hughes, S. G. (2011). Vicia, Chapter 14, C. Kole (Ed.). Wild Crop Relatives: Genomic and Breeding Resources, Legume Crops and Forages, Springer Verlag, Heidelberg.
• Cremonini, R., Miotto, D., Api Ngu, M., Tota, D., Pignone, D., Blangiforti, S., & Venora, G. (1998a). Cytology of Vicia species 5: nuclear chromatin structure, karyomorphological analysis and DNA content in newly discovered relatives of Vicia faba L.: Vicia kalakhensis Khattab, Maxted & Bisby and Vicia eristalioides Maxted. Cytologia, 63, 371-379.
• Cremonini, R., Ruffini, Castiglione, M., Venora, G., Blangiforti, S., Lo Savio, F. P., & Pignone, D. (1998b). Cytology of Vicia species 6: nuclear chromatin organization, karyomorphological analysis and DNA amount in Vicia serratifolia Jacq. Caryologia, 51, 195-205.
• Davis, P. H. (1970). Vicia L. Flora of Turkey and East Aegean Islands (Vol. 3). Edinburgh University Press, Edinburgh, U.K.
• Emre, İ. (2011). Determination of Genetic Diversity in the Vicia L. (section Vicia) by Using SDS-PAGE. Pakistan Journal of Botany, 43(3), 1429-1432.
• Enneking, D., & Maxted, N. (1995). Narbon bean (Vicia narbonensis L.). Evolution of Crop Plants, 2nd ed. Smartt, J., Simmonds, N. W., Longman: London, 316-321.
• Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
• Fennel, S. R., Powell, W., Wright, F., Ramsay, G., & Waugh, R. (1998). Phylogenetic relationships between Vicia faba (Fabaceae) and related species inferred from chloroplast trnL sequences. Plant Systematics and Evolution, 212, 247-259.
• Frediani, M., Sassoli, O., & Cremonini, R. (1992). Nuclear DNA characterization of two species of Vicia: V. bithynica L. and V. narbonensis L. Biologia Plantarum, 34, 335-344.
• Frediani, M., Maggini, F., Gelati, M. T., & Cremonini, R. (2004). Repetitive DNA sequences as probes for phylogenetic analysis in Vicia genus. Caryologia, 57(4), 379-386.
• Freeman, S., & Herron, J. C. (1999). Evrimsel Analiz, Çıplak, B., Başıbüyük. H. H., Karaytuğ, S., & Gündüz, İ. (Eds.). Palme Publishing, 28-29, 438-449.
• Foladi, F. Z., Salimpour, F., Sharifnia, F., & Ghanavati, F. (2013). Phylogenetic study of tribe Vicieae based on Internal Transcribed Spacer (ITS). Annals of Biological Research, 4(1), 75-79.
• Gunn, C. R. (1980). Genus Vicia with notes about Tribe Vicieae (Fabaceae) in Mexico and Central America. United States Department of Agriculture, Printing Office Washington D.C. 20402, 1-48.
• Inceer, H., & Hayırlıoğlu-Ayaz, S. (2005). Giemsa C-banded karyotypes of Vicia cracca L. subsp. cracca and V. bithynica L. Turkish Journal of Botany, 29, 311-316.
• Jaaska, V. (2008). Isozymes Evidence on the Specific Distinctness and Phylogenetic Position of Vicia incisa (Fabaceae). Central European Journal of Biology, 3(2), 169-176.
• Kahraman, A., Binzat, O. K., & Doğan, M. (2013). Pollen morphology of some taxa of Vicia L. subgenus Vicia (Fabaceae) Turkey. Plant Systematics and Evolution, 299, 1749-1760.
• Kelchner, S. A. (2000). The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden, 87, 482-498.
• Kimura, M. A. (1980). Simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
• Kress, W. J., Liu, A.-Z., Newman, M., & Li, Q. J. (2005). The molecular phylogeny of Alpinia (Zingiberaceae): a complex and polyphyletic genus of gingers. American Journal of Botany, 92(1), 167-178.
• Kupicha, F. K. (1976). The infrageneric structure of Vicia L. Notes Roy Bot Garden Edinburgh, 34, 287-326.
• Kupicha, F.K. (1981). Vicieae. In: Polhill R.M. & Raven P.H. (eds) Advances in Legume. Systematics, part 1. Ministry of Agriculture, Fisheries and Food, London, 377-381.
• Lefort, F., Lally, M., Thompson, D., & Douglas, G. C. (1998). Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at TrullynalIy, Ireland. Silvae Genetica, 47, 257-262.
• Leht, M. (2009). Phylogenetics of Vicia (Fabaceae) based on morphological data. Feddes Repertorium, 120(7-8), 379-393.
• Lorenzetti, F., Falcinelli, M., & Veronesi, F. (1994). Miglioramento Genetico delle Piante Agrarie. Italy: Edagricole, p. 328.
• Lorenzetti, F., Salvatore, C., & Veronesi, F. (1996). Genetica Agraria. Italy: Patron, 456.
• Maggini, F., Cremonini, R., Zolfino, C., Tucci, G. F., D'Ovidio, R., Delre, V., DePace, C., Scarascia Mugnozza, G. T., & Cionini, P. G. (1991). Structure and chromosomal localization of DNA sequences related to ribosomal subrepeats in Vicia faba. Chromosoma, 100, 229-234.
• Naranjo, C. A., Ferrari, M. R., Palermos. A. M., & Poggio, L. (1998). Karyotype, DNA content and meiotic behaviour in five South American species of Vicia (Fabaceae). Annals of Botany, 82, 757-764.
• Navratilova, A., Neumann, P., & Macas, J. (2003). Karyotype Analysis of Four Vicia species using in situ Hybridization with Repetitive Sequences. Annals of Botany, 91, 921- 926.
• Potokina, E. K., Tomooka, N., Vaughan, D. A., Alexandrova, T., & Xu, R. Q. (1999). Phylogeny of Vicia (Fabaceae) based on analysis of RAPDs and RFLP of PCR amplified chloroplast genes. Genetic Resources and Crop Evolution, 46, 149-161.
• Roze, I., & Rurane, I. (2013). Revision of genus Vicia L. in the flora of Latvia, Acta Biologica Universitatis Daugavpiliensis, 13(1), 85-93.
• Schaefer, H., Hechenleitner, P., Santos-Guerra, A., Menezes de Sequeira, M., Pennington, T. R., Kenicer, G., & Carine, A. M. (2012). Systematic, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BioMed Central Evolutionary Biology, 12, 250.
• Shaw, J., Lickey, E. B., Schilling, E. E., & Small, R. L. (2006). Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany, 94(3), 275-288.
• Simpson, M. G. 2012. Plant Systematics (2. Ed. ), Aytaç, Z. (Ed.), Nobel Publishing.
• Small, R. L., Cronn, R. C., & Wendell, J. F. (2004). Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany, 17, 145-170.
• Soltis, D. E., Soltis, P. S., & Milligan, B. G. (1992). Intra specific chloroplast DNA variation: systematics and phylogenetic implications. In: Soltis, P. S., Soltis, D. E. (Eds.) Molecular plant systematics, Chapman and Hall, New York, 117-150.
• Steele, K. P., & Wojciechowski, M. F. (2003). Phylogenetic analyses of tribes Trifolieae, Vicieae, based on sequences of the plastid gene (matK) (Papilionoidae: Leguminosae). In: Klitgaard, B. B., & Bruneau A. (Eds). Advance in Legume Systematic, part 10, Higher Level Systematics, Royal Botanic Garden, Kew.
• Taberlet, P., Gielly, L., Pantaou, G., & Bouvet, J. (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17, 1105-1109.
• Tabur, S., Civelek, Ş., & Bağcı, E. (2002). Cytotaxonomic studies on some Vicia L. Species Growing in the Eastern Mediterranean and Southern Aegean Regions II. Acta Botanica Hungarica, 44(1–2), 185-204.
• Van de Wouw, M., Maxted, N., Chabane, K., & Ford-Lloyd, B. V. (2001). Molecular taxonomy of Vicia ser. Vicia based on amplified fragment length polymorphisms. Plant Systematics and Evolution, 229, 91-105.
• Venora, G., Blangiforti, S., Frediani, M., Maggini, F., Gelati, M. T., Ruffini, C. M., & Cremonini, R. (2000). Nuclear DNA contents, rDNAs, chromatin organization and karyotype evolution in Faba section of the Vicia genus. Protoplasma, 213, 118-125.
• Vural, M. (2000). Vicia L. In: Güner, A., Özhatay, N, Ekim, T., & Başer, K. H. C. (Eds.). Flora of Turkey and the East Aegean Islands (Vol. 11), 89-92, Edinburgh: Edinburgh University Press.
• Weber, L. H., & Schifino-Wittmann, M. T. (1999). The Vicia sativa L. aggregate (Fabaceae) in Southern Brazil. Genetic Research and Crop Evolution, 46, 207-211.
• White, T. J., Burns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Application, Innis, M., Gelfand, D., Sninsky, J., White, T. (Eds.), Academic Press, San Diego, 315-322.