Phylogenetic analysis of Kars' endemic plant species through amplification of the 26S rDNA gene region

Asiye Uluğ; Funda Özdemir Değirmenci

doi:10.46309/biodicon.2024.1411165

Research Article

Phylogenetic analysis of Kars' endemic plant species through amplification of the 26S rDNA gene region

Year 2024, Volume: 17 Issue: 3, 235 - 242

Asiye Uluğ , Funda Özdemir Değirmenci

https://doi.org/10.46309/biodicon.2024.1411165

Abstract

Phylogenetic analysis of Kars' endemic plant species through amplification of the 26S rDNA gene region
Asiye Uluğ1*, Funda Özdemir Değirmenci2
ORCID: 0000-0001-5524-8431; 0000-0002-8875-0273

1 Department of Biology, Faculty of Science and Literature, Kafkas University, Kars, Türkiye
2 Department of Crop Science, Faculty of Agriculture, Ahi Evran University, Kırşehir, Türkiye

Abstract
The province of Kars, hosting 16% of Türkiye's plant cover, exhibits a high degree of floral diversity, including 71 endemic species. These species are located at the intersection of Türkiye's Caucasian lands, the Iran-Turan, Euro-Siberian, and Mediterranean flora regions. In this study, the 26S rDNA region of 14 endemic plant species sampled from Kars was amplified, and sequence data were obtained. NCBI GenBank database searches confirmed the first-time sequencing of the 26S rDNA gene region for these endemic plant species. The molecular characteristics of the 26S rDNA region of the 14 endemic plant species were examined, providing significant genetic data on the diversity and evolutionary relationships of endemic plants. Comparative analysis of the 26S rDNA sequences of the studied endemic species revealed notable genetic relationships within these plant groups, uncovering considerable variations among the species. The observed high polymorphism in the 26S rDNA region suggests its potential for accurate species identification. The genetic data obtained in this study have the potential to contribute to genetic research for the conservation of endemic species and biodiversity, emphasizing the importance of exploring and documenting the genetic uniqueness of endemic species. Furthermore, the genetic data obtained not only contribute to understanding the phylogenetic relationships among endemic species but also have implications for preserving and sustaining biological diversity by providing molecular identity to endemic plants in international databases.

Keywords: Kars, endemic, 26S rDNA, diversity, conservation

----------  ----------

Kars’ın endemik bitki türlerinin 26S rDNA gen bölgesi amplifikasyonu ile filogenetik analizi
Özet
Türkiye'nin bitki örtüsünün %16'sine ev sahipliği yapan Kars ili, 71'i endemik olmak üzere yüksek oranda floral çeşitliliğe sahiptir. Bu türler, Türkiye'nin Kafkas toprakları, İran-Turan, Euro-Sibirya ve Akdeniz bitki coğrafyasının kesişim noktasında bulunmaktadır. Bu çalışmada, Kars ilinden örneklenen 14 endemik bitki türünün 26S rDNA bölgesi amplifiye edilerek sekans verileri elde edilmiştir. NCBI GenBank veri tabanı eşleştirmeleri bu endemik bitki türlerinin 26S rDNA gen bölgesinin ilk defa sekanslandığını göstermiştir. 14 endemik bitki türünün 26S rDNA bölgesinin moleküler özellikleri incelenerek, endemik bitkilerin genetik çeşitlilikleri ve evrimsel ilişkileriyle ilgili önemli genetik veriler elde edilmiştir. Çalışılan endemik türlerin 26S rDNA dizilerinin karşılaştırılması, bu bitki grupları arasında önemli genetik ilişkileri ortaya koyarak, türler arasında dikkate değer varyasyonları açığa çıkarmıştır. Yüksek polimorfizm 26S rDNA bölgesinin doğru tür tanımlamasında ki potansiyelini göstermiştir. Bu çalışmada elde edilen genetik veriler, endemik türlerin ve biyoçeşitliliğin korunmasına yönelik genetik araştırmalara katkıda bulunma potansiyeline sahiptir ve endemik türlerin genetik benzersizliğinin keşfedilmesinin ve belgelenmesinin önemini açığa çıkarmaktadır. Ayrıca elde edilen genetik veriler, endemik türler arasındaki filogenetik ilişkilerin anlaşılmasına katkı sağlamasının yanı sıra, uluslarası veri tabanlarında endemik bitkilere moleküler kimlik vermede kullanılabileceğinden biyolojik çeşitliliğin korunması ve sürdürülebilir olması açısından önem arz etmektedir.

Anahtar kelimeler: Kars, endemik, 26S rDNA, çeşitlilik, koruma

Keywords

Kars, endemic, 26S rDNA, diversity, conservation

Ethical Statement

There is no ethical statement.

Supporting Institution

KAFKAS UNİVERSITY

Project Number

2023-FM-35

Thanks

We express our gratitude to Assistant Professor Dr. Gül Esma Akdoğan for her invaluable assistance during the field trip

References

[1] Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A., & Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature, 403(6772), 853-858. https://doi.org/10.1038/35002501
[2] Vellend, M., Baeten, L., Becker-Scarpitta, A., Boucher-Lalonde, V., McCune, J. L., Messier, J., Myers-Smith, I. H., & Saxet, D. F. (2013). Plant biodiversity changed across scales during the Anthropocene. Annual Review of Plant Biology, 64, 753-776. https://doi.org/ 10.1146/annurev-arplant-042916-040949
[3] CBOL Plant Working Group. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), 12794-12797. https://doi.org/10.1073/pnas.0905845106
[4] Sgrò, C. M., Lowe, A. J., & Hoffmann, A. A. (2011). Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications, 4(2), 326-337. https://doi.org/10.1111/j.1752-4571.2010.00157.x
[5] Chase, M.W., Salamin, N., Wilkinson, M., Dunwell, J.M., Kesanakurthi, R. P., Haider, N., & Savolainen, V. (2005). Land plants and DNA barcodes: short‐term and long‐term goals. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1889-1895. https://doi.org/10.1098/rstb.2005.1720
[6] Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Siripun, K.C., Winder, C.T., Schilling, E.E., & Small, R.L. (2005). The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany, 92(1), 142-166. https://doi.org/10.3732/ajb.92.1.142.
[7] Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270, 313–321. https://doi.org/10.1098/rspb.2002.2218.
[8] Hollingsworth, P. M., Li, D. Z., van der Bank, M., & Twyford A. D. (2016). Telling plant species apart with DNA: from barcodes to genomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1702):20150338. https://doi.org/10.1098/rstb.2015.0338
[9] Kuzoff, R. K., Sweere, J. A., Soltis, D. E., Soltis, P. S., & Zimmer, E. A. (1998). The phylogenetic potential of entire 26S rDNA sequences in plant. Molecular Biology and Evolution, 15, 251–263. https://doi.org/10.1093/oxfordjournals.molbev.a025922
[10] Soltis, D. E., Kuzoff, R. K., Mort, M. E., Zanis, M., Fishbein, M., Hufford, L., Koontz, J., & Arroyo, M. K. (2001). Elucidating deep-level phylogenetic relationships in Saxifragaceae using sequences for six chloroplastic and nuclear DNA regions. Annals of the Missouri Botanical Garden, 88, 669–693. https://doi.org/10.2307/3298639
[11] Markos, S., & Baldwin, B. G. (2002). Structure, molecular evolution, and phylogenetic utility of the 5′ regions of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Asteraceae). Molecular Phylogenetics and Evolution, 23,2. https://doi.org/10.1016/S1055-7903(02)00004-0.
[12] Güneş, F., & Özba, B. (2014). Kars çiçekleri. Kars: Kafkas Üniversitesi Yayınları.
[13] Ekim, T., Koyuncu, M., Vural, M., Duman, H., Aytaç, Z., & Adıgüzel, N. (2000). Türkiye bitkileri kırmızı kitabı. Türkiye’nin tehlike altındaki nadir ve endemik bitkileri. Ankara: Türkiye Tabiatını Koruma Derneği Yayınları.
[14] Özhatay, N. (2006). Türkiye’nin BTC boru hattı boyunca önemli bitki alanları. İstanbul: İstanbul Üniversitesi Yayınları.
[15] Kistler, L. (2012). Ancient DNA extraction from plants. Methods of Molecular Biology, 840:71–79. https://doi:10.1007/978-1- 61779-516-9_10
[16] Alvarez, I., & Wendel, J. F. (2003). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29(3):417–434. https://doi.org/10.1016/s1055-7903(03)00208-2
[17] Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
[18] Thompson, J. D., Higgins, D. G., Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research, 22(22):4673–4680. https://doi.org/10.1093/nar/22.22.4673
[19] Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6):1547–1549. https://doi:10.1093/molbev/msy096
[20] The website of National Center for Biotechnology Information (NCBI). (2023). Retrieved from https://www.ncbi.nlm.nih.gov/genbank/
[21] Saitou, N., & Nei, M. (1987). The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4: 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
[22] Tajima, F., & Nei, M. (1984). Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution, 1(3):269-85. https://doi: 10.1093/oxford journals molbev.a040317
[23] Benton, M. J., Donoghue, P. C., Asher, R. J., Friedman, M., Near, T. J., & Vinther, J. (2015). Constraints on the timescale of animal evolutionary history. Paleontological Society Papers, 21: 3-51.
[24] Heyduk, K., Moreno-Villena, J. J., Gilman, I. S., Christin, P. A., & Edwards, E. J. (2019). The genetics of convergent evolution: insights from plant photosynthesis. Nature Review Genetics. 20(8):485-493. https://doi: 10.1038/s41576-019-0107-5
[25] Wang, W., Zhang, X., Garcia, S., Leitch, A. R., & Kovarik, A. (2023). Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity 131, 179–188. https://doi:10.1038/s41437-023-00634-5
[26] Yılmaz Sancar, P., İçen Taşkın, I., Kursat, M., Munzuroğlu, Ö. (2021). Phylogenetic analysis for Endemic Fritillaria baskilensis Behçet (Liliaceae): Evidence from cpDNA “trn” sequences. Biyolojik Çeşitlilik Ve Koruma, 14(3), 431-441. https://doi.org/10.46309/biodicon.2021.963174 [27] Sözen, E., & Yücel, E. (2015). Determination of genetic relationships between some endemic Salvia species using RAPD markers. Biyolojik Çeşitlilik Ve Koruma, 8(3), 248-253.

Kars’ın endemik bitki türlerinin 26S rDNA gen bölgesi amplifikasyonu ile filogenetik analizi

Year 2024, Volume: 17 Issue: 3, 235 - 242

Asiye Uluğ , Funda Özdemir Değirmenci

https://doi.org/10.46309/biodicon.2024.1411165

Abstract

Keywords

Kars, endemik, 26S rDNA, çeşitlilik, koruma

Project Number

2023-FM-35

References

[1] Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A., & Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature, 403(6772), 853-858. https://doi.org/10.1038/35002501
[2] Vellend, M., Baeten, L., Becker-Scarpitta, A., Boucher-Lalonde, V., McCune, J. L., Messier, J., Myers-Smith, I. H., & Saxet, D. F. (2013). Plant biodiversity changed across scales during the Anthropocene. Annual Review of Plant Biology, 64, 753-776. https://doi.org/ 10.1146/annurev-arplant-042916-040949
[3] CBOL Plant Working Group. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), 12794-12797. https://doi.org/10.1073/pnas.0905845106
[4] Sgrò, C. M., Lowe, A. J., & Hoffmann, A. A. (2011). Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications, 4(2), 326-337. https://doi.org/10.1111/j.1752-4571.2010.00157.x
[5] Chase, M.W., Salamin, N., Wilkinson, M., Dunwell, J.M., Kesanakurthi, R. P., Haider, N., & Savolainen, V. (2005). Land plants and DNA barcodes: short‐term and long‐term goals. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1889-1895. https://doi.org/10.1098/rstb.2005.1720
[6] Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Siripun, K.C., Winder, C.T., Schilling, E.E., & Small, R.L. (2005). The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany, 92(1), 142-166. https://doi.org/10.3732/ajb.92.1.142.
[7] Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270, 313–321. https://doi.org/10.1098/rspb.2002.2218.
[8] Hollingsworth, P. M., Li, D. Z., van der Bank, M., & Twyford A. D. (2016). Telling plant species apart with DNA: from barcodes to genomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1702):20150338. https://doi.org/10.1098/rstb.2015.0338
[9] Kuzoff, R. K., Sweere, J. A., Soltis, D. E., Soltis, P. S., & Zimmer, E. A. (1998). The phylogenetic potential of entire 26S rDNA sequences in plant. Molecular Biology and Evolution, 15, 251–263. https://doi.org/10.1093/oxfordjournals.molbev.a025922
[10] Soltis, D. E., Kuzoff, R. K., Mort, M. E., Zanis, M., Fishbein, M., Hufford, L., Koontz, J., & Arroyo, M. K. (2001). Elucidating deep-level phylogenetic relationships in Saxifragaceae using sequences for six chloroplastic and nuclear DNA regions. Annals of the Missouri Botanical Garden, 88, 669–693. https://doi.org/10.2307/3298639
[11] Markos, S., & Baldwin, B. G. (2002). Structure, molecular evolution, and phylogenetic utility of the 5′ regions of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Asteraceae). Molecular Phylogenetics and Evolution, 23,2. https://doi.org/10.1016/S1055-7903(02)00004-0.
[12] Güneş, F., & Özba, B. (2014). Kars çiçekleri. Kars: Kafkas Üniversitesi Yayınları.
[13] Ekim, T., Koyuncu, M., Vural, M., Duman, H., Aytaç, Z., & Adıgüzel, N. (2000). Türkiye bitkileri kırmızı kitabı. Türkiye’nin tehlike altındaki nadir ve endemik bitkileri. Ankara: Türkiye Tabiatını Koruma Derneği Yayınları.
[14] Özhatay, N. (2006). Türkiye’nin BTC boru hattı boyunca önemli bitki alanları. İstanbul: İstanbul Üniversitesi Yayınları.
[15] Kistler, L. (2012). Ancient DNA extraction from plants. Methods of Molecular Biology, 840:71–79. https://doi:10.1007/978-1- 61779-516-9_10
[16] Alvarez, I., & Wendel, J. F. (2003). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29(3):417–434. https://doi.org/10.1016/s1055-7903(03)00208-2
[17] Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
[18] Thompson, J. D., Higgins, D. G., Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research, 22(22):4673–4680. https://doi.org/10.1093/nar/22.22.4673
[19] Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6):1547–1549. https://doi:10.1093/molbev/msy096
[20] The website of National Center for Biotechnology Information (NCBI). (2023). Retrieved from https://www.ncbi.nlm.nih.gov/genbank/
[21] Saitou, N., & Nei, M. (1987). The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4: 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
[22] Tajima, F., & Nei, M. (1984). Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution, 1(3):269-85. https://doi: 10.1093/oxford journals molbev.a040317
[23] Benton, M. J., Donoghue, P. C., Asher, R. J., Friedman, M., Near, T. J., & Vinther, J. (2015). Constraints on the timescale of animal evolutionary history. Paleontological Society Papers, 21: 3-51.
[24] Heyduk, K., Moreno-Villena, J. J., Gilman, I. S., Christin, P. A., & Edwards, E. J. (2019). The genetics of convergent evolution: insights from plant photosynthesis. Nature Review Genetics. 20(8):485-493. https://doi: 10.1038/s41576-019-0107-5
[25] Wang, W., Zhang, X., Garcia, S., Leitch, A. R., & Kovarik, A. (2023). Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity 131, 179–188. https://doi:10.1038/s41437-023-00634-5
[26] Yılmaz Sancar, P., İçen Taşkın, I., Kursat, M., Munzuroğlu, Ö. (2021). Phylogenetic analysis for Endemic Fritillaria baskilensis Behçet (Liliaceae): Evidence from cpDNA “trn” sequences. Biyolojik Çeşitlilik Ve Koruma, 14(3), 431-441. https://doi.org/10.46309/biodicon.2021.963174 [27] Sözen, E., & Yücel, E. (2015). Determination of genetic relationships between some endemic Salvia species using RAPD markers. Biyolojik Çeşitlilik Ve Koruma, 8(3), 248-253.

There are 26 citations in total.

Details

Primary Language	English
Subjects	Genetics (Other)
Journal Section	Research Articles
Authors	Asiye Uluğ 0000-0001-5524-8431 Funda Özdemir Değirmenci 0000-0002-8875-0273
Project Number	2023-FM-35
Early Pub Date	September 13, 2024
Publication Date
Submission Date	December 28, 2023
Acceptance Date	February 19, 2024
Published in Issue	Year 2024 Volume: 17 Issue: 3

Cite

APA	Uluğ, A., & Özdemir Değirmenci, F. (2024). Phylogenetic analysis of Kars’ endemic plant species through amplification of the 26S rDNA gene region. Biological Diversity and Conservation, 17(3), 235-242. https://doi.org/10.46309/biodicon.2024.1411165

Download Cover Image

Article Files

Full Text

❖ Abstracted-Indexed in
Web of Science {Zoological Records Indexed] Clavariate Analytic, Medical Reads (RRS), CrossRef;10.46309/biodicon.

❖ Libraries
Aberystwyth University; All libraries; Bath University; Birmingham University; Cardiff University; City University London; CONSER (Not UK Holdings); Edinburgh University; Essex University; Exeter University; Eskişehir Technical University Library; EZB Electronic Journals Library; Feng Chia University Library; GAZİ Gazi University Library; Glasgow University; HEC-National Digital Library; Hull University; Imperial College London; Kaohsinug Medical University Library; ANKOS; Anadolu University Library; Lancaster University; Libros PDF; Liverpool University; London Metropolitan University; London School of Economics and Political Science; Manchester University; National Cheng Kung University Library; National ILAN University Library; Nottingham University; Open University; Oxford University; Queen Mary,University of London;Robert Gordon University; Royal Botanic Gardens, Kew; Sheffield Hallam University; Sheffield University; Shih Hsin University Library; Smithsonian Institution Libraries; Southampton University; Stirling University; Strathclyde University; Sussex University; The National Agricultural Library (NAL); The Ohio Library and Information NetWork; Trinity College Dublin; University of Washington Libraries; Vaughan Memorial Library; York University..

❖ The article processing is free.

❖ Web of Science-Clarivate Analytics, Zoological Record
❖ This journal is a CrossRef;10.46309/biodicon. member

❖ Please visit ” http:// www.biodicon.com“ ; "https://dergipark.org.tr/en/pub/biodicon" for instructions about articles and all of the details about journal

❖ Correspondance Adres: Prof. Ersin YÜCEL, Sazova Mahallesi, Ziraat Caddesi, No.277 F Blok, 26005 Tepebaşı-Eskişehir/Türkiye
❖ E-posta / E-mail: biodicon@gmail.com;
❖ Web Address: http://www.biodicon.com; https://dergipark.org.tr/en/pub/biodicon
❖ Biological Diversity and Conservation/ Biyolojik Çeşitlilik ve Koruma
❖ ISSN 1308-5301 Print; ISSN 1308-8084 Online
❖ Start Date Published 2008
❖ © Copyright by Biological Diversity and Conservation/Biyolojik Çeşitlilik ve Koruma-Available online at www.biodicon.com/All rights reserved
❖ Publisher : ERSİN YÜCEL (https://www.ersinyucel.com.tr/)
❖ This journal is published three numbers in a year. Printed in Eskişehir/Türkiye.
❖ All sorts of responsibilities of the articles published in this journal are belonging to the authors
❖ Editör / Editor-In-Chief : Prof.Dr. Ersin YÜCEL, https://orcid.org/0000-0001-8274-7578