Öz
Endemic and rare plant taxa are critical components of biodiversity, playing key roles in ecosystem stability and resilience. However, these species are increasingly threatened by habitat loss, climate change, and anthropogenic pressures. Molecular approaches, particularly DNA barcoding, have become essential for accurate species identification and the assessment of genetic diversity. In this study, we evaluated the effectiveness of the partial 26S rDNA region as a DNA barcode marker for the molecular identification of 30 endemic and rare plant species from Kars Province, Türkiye. To our knowledge, this is the first application of the 26S rDNA region in these taxa. Sequence analyses revealed no exact matches in the GenBank database, indicating potential novelty and underscoring the scarcity of reference data. A total of 42 variable sites were identified across the sequences, and phylogenetic analyses largely clustered the species in accordance with their taxonomic families. Importantly, 30 novel barcode sequences were generated and submitted to public databases, offering valuable resources for future taxonomic, phylogenetic, and conservation-oriented studies. This work demonstrates the utility of partial 26S rDNA sequences for the molecular characterization of understudied endemic plants and provides a foundational step toward enhancing biodiversity documentation and conservation efforts in Türkiye.
Anahtar Kelimeler
Biodiversity endemic species Kars province 26S rDNA molecular identification phylogenetics
Etik Beyan
We have no conflicts of interest to disclose. The study was conducted in accordance with ethical values.
Destekleyen Kurum
KAFKAS UNVERSITY
Proje Numarası
2023-FM-35
Teşekkür
We would like to thank Prof. Dr. Zeki Kaya for allowing us to use the plant genetics laboratory at Middle East Technical University, Ankara, for some of our experiments. We thank to Asst. Prof. Dr. Muhammet Karadağ for his help in the field work.
Kaynakça
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. Journal of Molecular Biology 215(3): 403–410.
- Alvarez I, Wendel JF (2004). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29(3): 417–434.
- Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue M J (1995). The Its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden, 82(2): 247–77.
- Benton MJ, Donoghue PC, Asher R, Friedman M, Near TJ, Vinther J (2015). Constraints on the timescale of animal evolutionary history. Paleontological Society Papers 21: 3-51.
- CBOL Plant Working Group (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences 106(31): 12794-12797.
- Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, 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.
- 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. Türkiye Tabiatını Koruma Derneği Yayınları, Ankara.
- Gerbi SA (1985) Evolution of ribosomal DNA. In: Molecular Evolu-tionary Genetics (ed. MacIntyre RJ), pp. 419–517. Plenum, NewYork.
- Güneş F, Özba B (2014). Kars çiçekleri. Kafkas Üniversitesi Yayınları, Kars.
- Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences 270: 313–321.
- Heyduk K, Moreno-Villena JJ, Gilman IS, Christin PA, Edwards EJ (2019). The genetics of convergent evolution: insights from plant photosynthesis. Nature Review Genetics 20(8): 485-493.
- Hollingsworth PM, Li DZ, van der Bank M, Twyford D (2016). Telling plant species apart with DNA: from barcodes to genomes. Philosophical Transactions of the Royal Society B: Biological Sciences 371(1702): 20150338.
- Judd WC, Campbell CS, Kellogg E, Stevens P, Donoghue M (2015). Plant Systematics: A Phylogenetic Approach. Sinauer Associates, Sunderland, Massachusetts.
- 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.
- 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.
- Kuzoff RK, Sweere JA, Soltis DE, Soltis PS, Zimmer EA (1998). The phylogenetic potential of entire 26S rDNA sequences in plant. Molecular Biology and Evolution 15: 251–263.
- Linder CR, Goertzen LR, Heuvel BV, Francisco-Ortega J, Jansen RK. The complete external transcribed spacer of 18S-26S rDNA: amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied families. Mol Phylogenet Evol. 2000 Feb;14(2):285-303.
- Maia VH, Gitzendanner MA, Soltis PS, Wong GKS, Soltis DE (2014). Angiosperm phylogeny based on 18S/26S rDNA sequence data: Constructing a large data set using next-generation sequence data. Int J Plant Sci 175:613–50.
- Markos S, Baldwin BG (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.
- Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J (2000). Biodiversity hotspots for conservation priorities. Nature 403(6772): 853-858.
- Nasrollahi F, Kazempour-Osaloo S, Saadati N, Mozaffarian V, Zare-Maivan H (2019). Molecular phylogeny and divergence times of Onosma (Boraginaceae) based on nrDNA ITS and plastid rpl32-trnL(UAG) and trnH–psbA sequences. Nordic Jounrnal of Botany, 37:1.
- Nieto Feliner G, Rosselló JA. (2007). Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 44(2):911-9.
- Özhatay N (2006). Türkiye’nin BTC boru hattı boyunca önemli bitki alanları. İstanbul Üniversitesi Yayınları, İstanbul.
- Pang X, Liu C, Shi L, Liu R, Liang D, Li H, Chen S (2012). Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS ONE, 7(11), e48833.
- Saitou N, Nei M (1987). The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution 4: 406-425.
- Sgro CM, Lowe AJ, Hoffmann AA (2011). Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications 4(2): 326-337.
- Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (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.
- Shaw J, Lickey EB, Schilling EE, Small RL (2007). 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.
- Soltis DE, Kuzoff RK, Mort ME, 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.
- Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, et al. (2011). Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot 98(4):704-30. doi: 10.3732/ajb.1000404.
- Tajima F, Nei M (1984). Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 1(3): 269-85.
- The National Center for Biotechnology Information (NCBI) (2024). <https://www.ncbi.nlm.nih.gov/genbank/> Thompson JD, Higgins DG, Gibson TJ (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.
- Uyanık M, Kara ŞM, Gürbüz B, Özgen Y (2013). Türkiye’de Bitki Çeşitliliği ve Endemizm. Ekoloji 2013 Sempozyumu, Tekirdağ.
- Vellend M, Baeten L, Becker-Scarpitta A, Boucher-Lalonde V, McCune JL, Messier J, Myers-Smith I H, Saxet DF (2013). Plant biodiversity changed across scales during the Anthropocene. Annual Review of Plant Biology 64: 753-776.
- Wang W, Zhang, X, Garcia S, Leitch AR, Kovarik A (2023). Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity 131: 179–188.
Endemik bitkilerin filogenetik tanımlaması için kısmi 26S rDNA dizilerinin kullanımının değerlendirilmesi
Öz
Endemik bitki türleri, biyolojik çeşitliliğin hayati bileşenleridir ve ekosistem sürekliliğine ve direncine katkıda bulunurlar. Ancak bu türlerin birçoğu habitat tahribatı, iklim değişikliği ve insan faaliyetleri nedeniyle artan tehditlerle karşı karşıyadır. Moleküler yaklaşımlar, özellikle DNA barkodlama, endemik bitkilerin genetik çeşitliliğini tanımlamak ve anlamak için gerekli hale gelmiştir. Bu çalışmada, Kars ilinden 30 endemik bitki türünün filogenetik ilişkileri 26S rDNA gen bölgesi kullanılarak araştırılmıştır. Genomik DNA, modifiye CTAB yöntemi kullanılarak izole edilmiş ve 26S rDNA bölgesi bu türler için ilk kez başarılı bir şekilde çoğaltılmış ve dizilenmiştir. Dizi karşılaştırmaları, GenBank veri tabanında tam eşleşme göstermemiştir ve yakın akraba taksonlarla hizalama göstermiştir. Allium czelghauricum ve Fritillaria michailovskyi'nin kayda değer genetik farklılaşma sergilediği ve farklı evrimsel geçmişlere işaret eden toplam 42 değişken bölge tespit edilmiştir. Filogenetik analiz çoğu türü taksonomik ailelerine göre gruplandırmış, ancak muhtemelen taksonomik tutarsızlıklar veya yakınsak evrim nedeniyle bazı beklenmedik gruplanmalar gözlenmiştir. Bu çalışmanın sonuçları, Türkiye'nin endemik florasını anlamak için değerli genetik veriler sağlamakta ve biyoçeşitliliğin korunması için bir temel sunmaktadır.
Anahtar Kelimeler
Biyoçeşitlilik endemik türler Kars ili 26S rDNA moleküler tanımlama filogenetik
Proje Numarası
2023-FM-35
Kaynakça
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. Journal of Molecular Biology 215(3): 403–410.
- Alvarez I, Wendel JF (2004). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29(3): 417–434.
- Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue M J (1995). The Its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden, 82(2): 247–77.
- Benton MJ, Donoghue PC, Asher R, Friedman M, Near TJ, Vinther J (2015). Constraints on the timescale of animal evolutionary history. Paleontological Society Papers 21: 3-51.
- CBOL Plant Working Group (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences 106(31): 12794-12797.
- Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, 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.
- 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. Türkiye Tabiatını Koruma Derneği Yayınları, Ankara.
- Gerbi SA (1985) Evolution of ribosomal DNA. In: Molecular Evolu-tionary Genetics (ed. MacIntyre RJ), pp. 419–517. Plenum, NewYork.
- Güneş F, Özba B (2014). Kars çiçekleri. Kafkas Üniversitesi Yayınları, Kars.
- Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences 270: 313–321.
- Heyduk K, Moreno-Villena JJ, Gilman IS, Christin PA, Edwards EJ (2019). The genetics of convergent evolution: insights from plant photosynthesis. Nature Review Genetics 20(8): 485-493.
- Hollingsworth PM, Li DZ, van der Bank M, Twyford D (2016). Telling plant species apart with DNA: from barcodes to genomes. Philosophical Transactions of the Royal Society B: Biological Sciences 371(1702): 20150338.
- Judd WC, Campbell CS, Kellogg E, Stevens P, Donoghue M (2015). Plant Systematics: A Phylogenetic Approach. Sinauer Associates, Sunderland, Massachusetts.
- 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.
- 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.
- Kuzoff RK, Sweere JA, Soltis DE, Soltis PS, Zimmer EA (1998). The phylogenetic potential of entire 26S rDNA sequences in plant. Molecular Biology and Evolution 15: 251–263.
- Linder CR, Goertzen LR, Heuvel BV, Francisco-Ortega J, Jansen RK. The complete external transcribed spacer of 18S-26S rDNA: amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied families. Mol Phylogenet Evol. 2000 Feb;14(2):285-303.
- Maia VH, Gitzendanner MA, Soltis PS, Wong GKS, Soltis DE (2014). Angiosperm phylogeny based on 18S/26S rDNA sequence data: Constructing a large data set using next-generation sequence data. Int J Plant Sci 175:613–50.
- Markos S, Baldwin BG (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.
- Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J (2000). Biodiversity hotspots for conservation priorities. Nature 403(6772): 853-858.
- Nasrollahi F, Kazempour-Osaloo S, Saadati N, Mozaffarian V, Zare-Maivan H (2019). Molecular phylogeny and divergence times of Onosma (Boraginaceae) based on nrDNA ITS and plastid rpl32-trnL(UAG) and trnH–psbA sequences. Nordic Jounrnal of Botany, 37:1.
- Nieto Feliner G, Rosselló JA. (2007). Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 44(2):911-9.
- Özhatay N (2006). Türkiye’nin BTC boru hattı boyunca önemli bitki alanları. İstanbul Üniversitesi Yayınları, İstanbul.
- Pang X, Liu C, Shi L, Liu R, Liang D, Li H, Chen S (2012). Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS ONE, 7(11), e48833.
- Saitou N, Nei M (1987). The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution 4: 406-425.
- Sgro CM, Lowe AJ, Hoffmann AA (2011). Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications 4(2): 326-337.
- Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (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.
- Shaw J, Lickey EB, Schilling EE, Small RL (2007). 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.
- Soltis DE, Kuzoff RK, Mort ME, 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.
- Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, et al. (2011). Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot 98(4):704-30. doi: 10.3732/ajb.1000404.
- Tajima F, Nei M (1984). Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 1(3): 269-85.
- The National Center for Biotechnology Information (NCBI) (2024). <https://www.ncbi.nlm.nih.gov/genbank/> Thompson JD, Higgins DG, Gibson TJ (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.
- Uyanık M, Kara ŞM, Gürbüz B, Özgen Y (2013). Türkiye’de Bitki Çeşitliliği ve Endemizm. Ekoloji 2013 Sempozyumu, Tekirdağ.
- Vellend M, Baeten L, Becker-Scarpitta A, Boucher-Lalonde V, McCune JL, Messier J, Myers-Smith I H, Saxet DF (2013). Plant biodiversity changed across scales during the Anthropocene. Annual Review of Plant Biology 64: 753-776.
- Wang W, Zhang, X, Garcia S, Leitch AR, Kovarik A (2023). Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity 131: 179–188.
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Bitki Hücresi ve Moleküler Biyoloji, Bitki Bilimi (Diğer) |
| Bölüm | Araştırma Makaleleri |
| Yazarlar | |
| Proje Numarası | 2023-FM-35 |
| Erken Görünüm Tarihi | 27 Haziran 2025 |
| Yayımlanma Tarihi | 30 Haziran 2025 |
| Gönderilme Tarihi | 19 Şubat 2025 |
| Kabul Tarihi | 31 Mayıs 2025 |
| Yayımlandığı Sayı | Yıl 2025 Cilt: 8 Sayı: 1 |
Türk Biyoçeşitlilik Dergisi Creative Commons Alıntı-GayriTicari-Türetilemez 4.0 Uluslararası Lisansı ile lisanslanmıştır.