Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region

Ayşenur Kalmer; Ayten Dizkırıcı Tekpınar

doi:10.17776/csj.363294

TR EN

Centaurea Cinsine Ait Beş Türün trnT-L-F cpDNA Bölgesi Kullanılarak Filogenetik İlişkilerinin Belirlenmesi

Abstract

Asteraceae familyasına ait Centaurea L. cinsi sistematik açıdan tartışmaları barındıran ve son yıllarda gelişen moleküler tekniklerin ışığında taksonomik problemleri aydınlatılması gereken bir cinstir. Özellikle Centaurea depressa türünün taksonomik konumu tartışmalı olup bazı araştırmacılar tarafından Cyanus cinsinde olması gerektiği iddia edilmiştir. Bu problemi açığa kavuşturmak için, cinse ait beş türün (C. depressa, C. iberica, C. solstitialis, C. virgata, C. balsamita) filogenetik ilişkileri kloroplast DNA’sında bulunan ve filogenetik çalışmalarda tercih edilen trnT^(UGU) - trnL^(UAA)IGS, trnL5’- trnL3’ intron ve trnL^(UAA)- trnF^(GAA)IGS bölgeleri kullanılarak belirlenmeye çalışılmıştır. Cinse ait bazı türlerin DNA sekansları NCBI veri tabanından alınarak analizlere eklenmiş ve hem C. depressa’nın hem de çalışılan diğer dört türün cins içindeki evrimsel ilişkileri aydınlatılmaya çalışılmıştır. Maksimum Olasılık (ML) ve Maksimum Parsimoni (MP) metodlarıyla filogenetik ağaçlar oluşturulmuştur. trnT^(UGU) - trnL^(UAA) ve trnL5’- trnL3’ intron bölgeleri için oluşturulan ağaçlarda C. depressa türü diğer akraba türlerden filogenetik olarak ayrılmamıştır. trnL^(UAA)- trnF^(GAA)IGS bölgesinde yeterli kalitede sekanslar elde edilemediğinden çalışmamızda bu bölge detaylandırılmamıştır.

Keywords

Centaurea,filogeni,trnT(UGU) - trnL(UAA),trnL5’- trnL3’ intron,trnL(UAA) - trnF(GAA) IGS

Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region

Abstract

The genus Centaurea L., belonging to Asteraceae family, contains systematic controversies and these taxonomic problems must be illuminated in the light of the molecular techniques developed in recent years. Especially, taxonomic position of Centaurea depressa is controversial and moving of this species to Cyanus genus is claimed by several researchers. To solve this problem, phylogenetic relationships of five species (C. depressa, C. iberica, C. solstitialis, C. virgata, C. balsamita) were tried to be determined by using the trnT^(UGU) - trnL^(UAA), trnL5’- trnL3’ intron and trnL^(UAA)- trnF^(GAA)IGS regions which are found in the chloroplast DNA and are preferred for phylogenetic studies. DNA sequences of other species belonging to the genus Centaurea were retrieved from NCBI database and analyzed to clarify the evolutionary relationships of not only C. depressa but also the other four species. Phylogenetic trees were constructed by using Maximum Likelihood (ML) and Maksimum Parsimony (MP) methods. That’s why, the data obtained from the trnL-trnF region will not be shared. Centaurea depressa is not phylogenetically separated from other related species in the trees contructed by using trnT^(UGU) - trnL^(UAA) and trnL5’- trnL3’ intron regions. DNA sequences obtained from trnL^(UAA)- trnF^(GAA)IGS region are not clear so this region is not elaborated.

Keywords

Centaurea,phylogeny,trnT(UGU) - trnL(UAA) IGS,trnL5’-trnL3’ intron,trnL(UAA)-trnF(GAA) IGS

References

[1]. Susanna A., Garcia-Jacas N., Tribe Cardueae. In: Kadereit, J.W. & Jeffrey, C. (eds.) The families and genera of vascular plants 8. Springer-Verlag, Berlin 2007; 123-147.
[2]. Davis P.H., Flora of Turkey and The East Aegean Islands Vol. 10, Edinburgh University Press, Edinburgh 1988; p. 431-463.
[3]. Dittrich M., Cynareae systematic review. In: Heywood VH, Harborne JB, Turner BL, eds. The biology and chemistry of the Compositae London, New York, San Francisco: Academic Press 1977; 999-1015.
[4]. Bremer K., Asteraceae. Cladistics & classification. Portland 1994; Timber Press.
[5]. Wagenitz G, Hellwig FH., Evolution of characters and Phylogeny of the Centaureinae. In: Hind DJN, Beentje HG, eds. Compositae: Systematics. Proceedings of the International Compositae Con- ference, Kew Kew: Royal Botanic Gardens 1996; 491-510.
[6]. Alvarado J.V., Centaurea L. sect. Phrygia Pers.: Phylogeny and Biogeography 2011; Università degli Studi di Sassari (doktora tezi), Sassari Üniversitesi, İtalya.
[7]. Hilphold A., Vilatersana R., Susanna A., Meseguer S.A., Borsic I., Constantinidis T., Filigheddu R., Romaschenko K., Suarez-Santiago N.V., Tugay O., Uysal T., Pfeil E.B., Garcia-Jacas N. Phylogeny of the Centaurea group (Centaurea, Compositea)- geography is a better predictor than morphology Molecular Phylogenetics and Evolution 2014; 77: 195-215.
[8]. Garcia-Jacas N., Uysal T., Romashchenko, K., Suarez-santıago V.N., Ertuğrul K., Susanna A. Centaurea Revisited: A Molecular Survey of the Jacea Group. Annals of Botany 2006; 98: 741-753.
[9]. Garcia-Jacas N., Susanna A., Garnatje T., Vİlatersana R. Generic Delimitation and Phylogeny of the Subtribe Centaureinae (Asteraceae): A Combined Nuclear and Chloroplast DNA Analysis. Annals of Botany 2001; 87: 503-515.
[10]. Soltis D.E., Soltis P.S., Milligan B.G. 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 1992; 117–150.

[11]. Shaw J., Lickey E.B., Schilling E.E., Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III American J. Bot. 2006; 94:3 275-288.
[12]. Taberlet P., Gielly L., Pantaou G., Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA Plant Mol. Biol. 1991; 17: 1105-1109.
[13]. Kelchner Scot A. The evolution of non-coding chloroplast DNA and its application in plant systematics”, Chap. 87. Annals of the Missouri Botanical Garden 2000; 482-498.
[14]. Güner A., Aslan S., Ekim T., Vural M., Babaç M. T. Türkiye Bitkileri Listesi (Damarlı Bitkiler)”, İstanbul: Nezahat Gökyiğit Botanik Bahçesi ve Flora Araştırmaları Derneği Yayını. 2012.
[15]. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue”. Phytochemical Bulletin 1987; 19: 11-15.
[16]. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA 5: molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molec. Biol. Evol. 2011; 28: 2731-2739.
[17]. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees”. Molecular Biology and Evolution 1993; 10: 512-526.
[18]. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap”. Evolution 1985; 39: 783-791.
[19]. Font M., Garnatje T., Garcia-Jacas N., Susanna A. Delineation and Phylogeny of Centaurea sect. Acrocentron based on DNA sequence: a restoration of the genus Crocodylium and indirect evidence of introgression Plant Sistematic and Evolution 2002; 234: 15-26.
[20]. Dizkirici A., Köroğlu Z. Van İlinde Bulunan Centaurea Cinsine Ait Bazı Türlerinin Filogenetik İlişkilerinin ITS ve MatK Bölgeleri Kullanılarak Belirlenmesi 2017; DOI: 10.19113/sdufbed.39508

Details

Primary Language

English

Subjects

-

Journal Section

Research Article

Authors

Ayşenur Kalmer

Ayten Dizkırıcı Tekpınar ^*

Publication Date

December 8, 2017

Submission Date

May 17, 2017

Acceptance Date

November 21, 2017

Published in Issue

Year 2017 Volume: 38 Number: 4

DOI

https://doi.org/10.17776/csj.363294

IZ

https://izlik.org/JA37FE52NS

APA

Kalmer, A., & Dizkırıcı Tekpınar, A. (2017). Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region. Cumhuriyet Science Journal, 38(4), 52-59. https://doi.org/10.17776/csj.363294

AMA

1.Kalmer A, Dizkırıcı Tekpınar A. Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region. CSJ. 2017;38(4):52-59. doi:10.17776/csj.363294

Chicago

Kalmer, Ayşenur, and Ayten Dizkırıcı Tekpınar. 2017. “Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using TrnT-L-F CpDNA Region”. Cumhuriyet Science Journal 38 (4): 52-59. https://doi.org/10.17776/csj.363294.

EndNote

Kalmer A, Dizkırıcı Tekpınar A (December 1, 2017) Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region. Cumhuriyet Science Journal 38 4 52–59.

IEEE

[1]A. Kalmer and A. Dizkırıcı Tekpınar, “Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region”, CSJ, vol. 38, no. 4, pp. 52–59, Dec. 2017, doi: 10.17776/csj.363294.

ISNAD

Kalmer, Ayşenur - Dizkırıcı Tekpınar, Ayten. “Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using TrnT-L-F CpDNA Region”. Cumhuriyet Science Journal 38/4 (December 1, 2017): 52-59. https://doi.org/10.17776/csj.363294.

JAMA

1.Kalmer A, Dizkırıcı Tekpınar A. Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region. CSJ. 2017;38:52–59.

MLA

Kalmer, Ayşenur, and Ayten Dizkırıcı Tekpınar. “Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using TrnT-L-F CpDNA Region”. Cumhuriyet Science Journal, vol. 38, no. 4, Dec. 2017, pp. 52-59, doi:10.17776/csj.363294.

Vancouver

1.Ayşenur Kalmer, Ayten Dizkırıcı Tekpınar. Determination of Phylogenetic Relationships of Five Species of Centaurea Genus by Using trnT-L-F cpDNA Region. CSJ. 2017 Dec. 1;38(4):52-9. doi:10.17776/csj.363294

Cited By

Genetic Diversity and Phylogenetic Analyzes of Laurus nobilis L. (Lauraceae) Populations Revealed Chloroplast (cpDNA) trnL Intron and trnL-F Region

International Journal of Fruit Science

https://doi.org/10.1080/15538362.2019.1707745

Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences

International Journal of Fruit Science

https://doi.org/10.1080/15538362.2020.1828223

Microscopic Analysis of Anatomical and Taxonomic Characteristics in Some Centaurea Species

Microscopy Research and Technique

https://doi.org/10.1002/jemt.70068

As of 2026, Cumhuriyet Science Journal will be published in six issues per year, released in February, April, June, August, October, and December