SavedAdd your journal

Journals / Gazi University Journal of Science / 2026 / Volume: 39 Issue: 3

Preliminary Phylogenetic Analysis and DNA Barcoding of Endemic and Threatened Silene species in Türkiye using ITS and rps16 Intron Markers

ITS ve rps16 İntron Bölgeleri Kullanılarak Türkiye'deki Endemik ve Tehdit Altındaki Silene Türlerinin Ön Filogenetik Analizi ve DNA Barkodlaması

Fevzi Özgökçe(VAN YUZUNCU YIL UNIVERSITY)0000-0002-3119-8561
Şuheda Aldemir Terman(VAN YUZUNCU YIL UNIVERSITY)0000-0002-1244-9716
Ayten Dizkırıcı(VAN YUZUNCU YIL UNIVERSITY)0000-0002-0578-5092
Pages
—
Publication Date
2026-09-01
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

This study represents the first integrated DNA barcoding and phylogenetic analysis of endangered Turkish Silene taxa, highlighting the utility of combined ITS and rps16 intron markers for species identification and resolving phylogenetic relationships, while providing a genetic baseline for the conservation of these rare taxa.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:The genus Silene (Caryophyllaceae) is one of the most species-rich groups in Türkiye, with 180 recognized taxa, 63 of which are endemic.
📊
Key Findings & Data:Here, we investigated twelve Turkish Silene taxa, including four endemics, using nuclear ribosomal ITS and chloroplast rps16 intron sequences.
💡
Conclusion & Impact:This study represents the first integrated DNA barcoding and phylogenetic analysis of endangered Turkish Silene taxa, highlighting the utility of combined ITS and rps16 intron markers for species identification and resolving phylogenetic relationships, while providing a genetic baseline for the conservation of these rare taxa.
🔬Design:Research Article
📍Scope:Comprehensive Sample
⚙️Variables:Endemic · Molecular phylogeny · Silene

Abstract

The genus Silene (Caryophyllaceae) is one of the most species-rich groups in Türkiye, with 180 recognized taxa, 63 of which are endemic. Despite their ecological and conservation importance, the phylogenetic relationships of many endemic and threatened taxa remain unresolved. Here, we investigated twelve Turkish Silene taxa, including four endemics, using nuclear ribosomal ITS and chloroplast rps16 intron sequences. The concatenated dataset (1517 bp) contained 108 polymorphic sites and provided strong phylogenetic signal. Bayesian analyses revealed two well-supported clades: (i) Lasiostemones, Sclerocalycine, and Nanosilene; and (ii) Spergulifoliae and Auriculatae. Notable markers included a unique 38-bp insertion in S. argaea and several section-specific substitutions. This study represents the first integrated DNA barcoding and phylogenetic analysis of endangered Turkish Silene taxa, highlighting the utility of combined ITS and rps16 intron markers for species identification and resolving phylogenetic relationships, while providing a genetic baseline for the conservation of these rare taxa.

Özet

Silene cinsi (Caryophyllaceae), 63'ü endemik olmak üzere 180 takson ile Türkiye'deki tür bakımından en zengin gruplardan biridir. Ekolojik ve koruma açısından önemlerine rağmen, birçok endemik ve tehdit altındaki taksonun filogenetik ilişkileri henüz çözülmemiştir. Bu çalışmada, 4'ü endemik olmak üzere Türkiyede yetişen 12 Silene taksonu, çekirdek ribozomal ITS ve kloroplast rps16 intron dizileri kullanılarak incelenmiştir. Birleştirilmiş veri seti (1517 bp), 108 polimorfik nukleotit içermekte ve güçlü filogenetik sinyal sağlamaktadır. Bayesyen analizleri iyi desteklenen iki klad ortaya koymuştur: (i) Lasiostemones, Sclerocalycine ve Nanosilene; ve (ii) Spergulifoliae ve Auriculatae. Önemli sonuçlar arasında S. argaea'da bulunan benzersiz bir 38-bp insersiyon ve birkaç seksiyona özgü substitüsyon yer almaktadır. Bu çalışma, nesli tehlike altındaki Türk Silene türlerinin ilk DNA barkod analizini temsil etmekte, ilişkilerin çözülmesinde kombine edilmiş ITS ve rps16 intron bölgelerinin faydasını vurgulamakta ve bu nadir taksonların korunması için genetik bir temel sağlamaktadır.

🔖

Cite This Article

Özgökçe, F., Terman, Ş. A., Dizkırıcı, A., *, A. D. (2026). Preliminary Phylogenetic Analysis and DNA Barcoding of Endemic and Threatened Silene species in Türkiye using ITS and rps16 Intron Markers. Gazi University Journal of Science, Volume: 39 Issue: 3. https://doi.org/10.35378/gujs.1908682

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (55)

  1. Hernández-Ledesma, P., Berendsohn, W. G., Borsch, Th., Mering, S. von, Akhani, H., Arias, S., Castañeda-Noa, I., Eggli, U., Eriksson, R., Flores-Olvera, H., Fuentes-Bazán, S., Kadereit, G., Klak, C., Korotkova, N., Nyffeler, R., Ocampo, G., Ochoterena, H., Oxelman, B., Rabeler, R. K., Sanchez, A., Schlumpberger, B. O. and Uotila, P., “A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales”, Willdenowia, 45: 281–383 (2015). DOI: https://doi.org/10.3372/wi.45.45301
  2. Greenberg, A. K., and Donoghue, M. J., “Molecular systematics and character evolution in Caryophyllaceae”, Taxon, 60(6): 1637–1652, (2011). DOI: https://doi.org/10.1002/tax.606009
  3. Bittrich, V., Caryophyllaceae. In: Kubitzki, J., “The Families and Genera of Vascular Plants Vol. 2”, Berlin: Springer, 206–236, (1993).
  4. Harbaugh, D. T., Nepokroeff, M., Rabeler, R. K., McNeill, J., Zimmer, E. A., and Wagner, W. L., “A new lineage-based tribal classification of the family Caryophyllaceae”, International Journal of Plant Sciences, 171(2): 185–198, (2010). DOI: https://doi.org/10.1086/648993
  5. Madhani, H., Rabeler, R., Pirani, A., Oxelman, B., Heubl, G., and Zarre, S., “Untangling phylogenetic patterns and taxonomic confusion in tribe Caryophylleae (Caryophyllaceae) with special focus on generic boundaries”, Taxon, 67(1): 83–112, (2018). DOI: https://doi.org/10.12705/671.6
  6. Rautenberg, A., Filatov, D., Svennblad, B., Heidari, N., and Oxelman, B., “Conflicting phylogenetic signals in the SIX1/Y1 gene in Silene”, BMC Evolutionary Biology, 8: 299, (2008). DOI: https://doi.org/10.1186/1471-2148-8-299
  7. Coode, M. J. E., and Cullen, J., [Silene L.] In: Davis, P. H. Flora of Turkey and the East Aegean Islands Vol. 2. Edinburgh: Edinburgh Univ Press, 179–242, (1967).
  8. Davis, P. H., Mill, R. R., and Tan, K., [Silene L.] In: Davis, P. H., Mill, R. R., and Tan, K., Flora of Turkey and the East Aegean Islands Vol. 10. Edinburgh: Edinburgh Univ Press, 76–81, (1988).
  9. Tan, K., and Vural, M., [Silene L.] In: Güner, A., Özhatay, N., Ekim, T., and Başer, K. H. C., Flora of Turkey and the East Aegean Islands, Vol. 11 (Suppl. II). Edinburgh: Edinburgh University Press, 50–53, (2000).
  10. Yıldız, K., [Silene L.] In: Güner, A., Yıldız, K., Vural, M., Kandemir, A., Menemen, Y., Yıldırım, H., Aslan, S., Çimen, A. Ö., Güner, I., Bona, G. E., and Gökmen, F. Ş., Resimli Türkiye Florası 17c: 130–463. İstanbul: ANG Vakfı Nezahat Gökyiğit Botanik Bahçesi Yayınları, (2024).
  11. Naciri, Y., Du Pasquier, P. E., Lundberg, M., Jeanmonod, D., and Oxelman, B., “A phylogenetic circumscription of Silene sect. Siphonomorpha (Caryophyllaceae) in the Mediterranean Basin”, Taxon, 66: 91–108, (2017). DOI: https://doi.org/10.12705/661.5
  12. Petri, A., and Oxelman, B., “Phylogenetic relationships within Silene (Caryophyllaceae) section Physolychnis”, Taxon, 60: 953–968, (2011). DOI: https://doi.org/10.1002/tax.604002
  13. Toprak, Z., Pfeil, B. E., Jones, G., Marcussen, T., Ertekin, A. S., and Oxelman, B., “Species delimitation without prior knowledge: DISSECT reveals extensive cryptic speciation in the Silene aegyptiaca complex (Caryophyllaceae)”, Molecular Phylogenetics and Evolution, 102: 1–8, (2016). DOI: https://doi.org/10.1016/j.ympev.2016.05.024
  14. Jafari, F., Zarre, S., Gholipour, A., Eggens, F., Rabeler, R. K., and Oxelman, B., “A new taxonomic backbone for the infrageneric classification of the species-rich genus Silene (Caryophyllaceae)”, Taxon, 69: 337–368, (2020). DOI: https://doi.org/10.1016/j.ympev.2016.05.024
  15. Martin, E., Tekin, M., Dirlik, G. M., and Türk, M., “Karyotype analysis of Silene muradica Caryophyllaceae”, Karaelmas Fen ve Mühendislik Dergisi, 9(1): 114–117, (2019). DOI: https://doi.org/10.7212/zkufbd.v9i1.1314
  16. Behçet, L., and Yapar, Y., “Silene hamzaoglui (Caryophyllaceae) için yeni popülasyonlar ve yeni bir sinonim”, Türler ve Habitatlar, 1(1): 7–13, (2020).
  17. Yıldız, K., Kuh, M., Tan, S., and Ay, G., “Türkiye’de yetişen bazı Silene L. türlerinin toprak özellikleri”, Biological Diversity and Conservation, 13(3): 252–263, (2020). DOI: https://doi.org/10.46309/biodicon.2020.753427
  18. Yılmaz Çıtak, B., and Dural, H., “Silene otites (L.) Wibel/Sinekkıran (Caryophyllaceae) türünün anatomik özellikleri”, Bağbahçe Bilim Dergisi, 8(1): 106–110, (2021). DOI: https://doi.org/10.35163/bagbahce.772537
  19. Tok, K. C., Hürkul, M. M., Bozkurt, N. N., Aysal, A. İ., and Yayla, Ş., “Investigation of phytochemicals in methanolic herba extract of Silene ruscifolia by LC-QTOF/MS and GC/MS”, Journal of Faculty of Pharmacy of Ankara University, 46(3): 827–838, (2022). DOI: https://doi.org/10.33483/jfpau.1133615
  20. Akpulat, H. A., and Işıksal, D. D., “Morpho-anatomical, palynological and karyological characterization of Silene commelinifolia var. ruscifolia (Caryophyllaceae)”, Turkish Journal of Biodiversity, 6(2): 103–119, (2023). DOI: https://doi.org/10.38059/biodiversity.1387502
  21. Şen, H., Bazı endemik Silene türlerinin incelenmesi. 1. Baskı. Konya: Eğitim Yayınevi. (2023)
  22. Fırat, M., “New record for the flora of Türkiye: Silene vivianii subsp. viscida (Caryophyllaceae)”, Türler ve Habitatlar, 5(1): 26–31, (2024). DOI: https://doi.org/10.53803/turvehab.1495279
  23. Parlakova Karagöz, F., Dursun, A., Dumlu, B., and Karaşal, M., “Colchicine-induced polyploidy and morphological changes in wild Silene compacta Fischer: Potential as an ornamental plant in Türkiye”, Journal of Biometry Studies, 4(2): 79–90, (2024). DOI: https://doi.org/10.61326/jofbs.v4i2.04
  24. Sevindik, E., “Türkiye'de yetişen Silene L. cinsinin Auriculatae ve seksiyonlarına ait türlerin ITS nrDNA dizilerine dayalı filogenetik ilişkileri”, Yüksek Lisans Tezi, Balıkesir Üniversitesi, Fen Bilimleri Enstitüsü, Biyoloji Ana Bilim Dalı, Balıkesir, (2011).
  25. Toprak, Z., “Investigation of the occurrence of Silene fuscata in Anatolia based on molecular analysis”, Commagene Journal of Biology, 7(2): 164–170, (2023). DOI: https://doi.org/10.31594/commagene.1404268
  26. Göçmen, M., Kaya, A. S., Aydınşakır, K., Özçelik, A., and Polat, İ., “Assessment of genetic diversity and relationships among Gypsophila and Silene species from Türkiye using SRAP markers”, KSU Journal of Agriculture and Nature, 28(1): 83–95, (2025). DOI: https://doi.org/10.18016/ksutarimdoga.vi.1398542
  27. Ali, M. A., Gyulai, G., Hidvegi, N., Kerti, B., Al Hemaid, F. M., Pandey, A. K., and Lee, J., “The changing epitome of species identification–DNA barcoding”, Saudi Journal of Biological Sciences, 21: 204–231, (2014). DOI: https://doi.org/10.1016/j.sjbs.2014.03.003
  28. Kolter, A., and Gemeinholzer, B., “Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases”, Genome, 64: 265–298, (2021). DOI: https://doi.org/10.1139/gen-2019-0198
  29. Safhi, F. A., Alshamrani, S. M., Fiteha, Y. G., and Abd El-Moneim, D., “DNA barcoding of endangered and rarely occurring plants in Faifa Mountains (Jazan, Saudi Arabia)”, Agriculture, 12: 1931, (2022). DOI: https://doi.org/10.3390/agriculture12111931
  30. Ghareb, H. E. S., and Abouseadaa, H. H., “In vitro propagation and DNA barcoding of the rare near endemic Plantago sinaica (Barnéoud) plant in Saint Katherine, Sinai”, Plant Cell Tissue and Organ Culture, 156: 69, (2024). DOI: https://doi.org/10.1007/s11240-024-02689-6
  31. Hebert, P. D. N., Floyd, R., Jafarpour, S., and Prosser, S. W. J., “Barcode 100K specimens: in a single nanopore run”, Molecular Ecology Resources, 25: e14028, (2025). DOI: https://doi.org/10.1111/1755-0998.14028
  32. Eggens, F., Jafari, F., Thollesson, M., Crameri, S., Zarre, S., and Oxelman, B., “Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section”, PhytoKeys, 159: 1–34, (2020). DOI: https://doi.org/10.3897/phytokeys.159.51500
  33. El-Banhawy, A., Nour, I. H., Acedo, C., ElKordy, A., Faried, A., Al-Juhani, W., Gawhari, A. M. H., Olwey, A. O., and Ellmouni, F. Y., “Taxonomic revisiting and phylogenetic placement of two endangered plant species: Silene leucophylla Boiss. and Silene schimperiana Boiss. (Caryophyllaceae)”, Plants, 10(4): 740, (2021). DOI: https://doi.org/10.3390/plants10040740
  34. Jin, D. P., Sim, S., Park, J. W., Choi, J. E., Yoon, J., Lim, C. E., and Kim, M. H., “Identification of the plant family Caryophyllaceae in Korea using DNA barcoding”, Plants (Basel), 12(10): 2060, (2023). DOI: https://doi.org/10.3390/plants12102060
  35. Letsiou, S., Madesis, P., Vasdekis, E., Montemurro, C., Grigoriou, M. E., Skavdis, G., Moussis, V., Koutelidakis, A. E., and Tzakos, A. G., “DNA barcoding as a plant identification method”, Applied Sciences, 14: 1415, (2024). DOI: https://doi.org/10.3390/app14041415
  36. Kartzinel, T. R., Hoff, H. K., Divoll, T. J., Littleford-Colquhoun, B. L., Anderson, H., Burak, M. K., Kuzmina, M. L., Musili, P. M., Rogers, H., Troncoso, A. J., and Kartzinel, R. Y., “Global availability of plant DNA barcodes as genomic resources to support basic and policy-relevant biodiversity research”, Molecular Ecology, 34: e17712, (2025). DOI: https://doi.org/10.1111/mec.17712
  37. Baldwin, B. G., Sanderson, M. J., Porter, J. M., Wojciechowski, M. F., Campbell, C. S., and Donoghue, M. J., “The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny”, Annals of the Missouri Botanical Garden, 82: 247–277, (1995). DOI: https://doi.org/10.2307/2399880
  38. Álvarez, I., and Wendel, J. F., “Ribosomal ITS sequences and plant phylogenetic inference”, Molecular Phylogenetics and Evolution, 29: 417–434, (2003). DOI: https://doi.org/10.1016/s1055-7903(03)00208-2
  39. Li, D. Z., Gao, L. M., Li, H. T., Wang, H., Ge, X. J., Liu, J. Q., Chen, Z. D., Zhou, S. L., Chen. S. L., Yang, J. B., Fu, C. X., Zeng, C. X., Yan, H. F., Zhu, Y. J., Sun, Y. S., Chen, S. Y., Zhao, L., Wang, K., Yang, T., and Duan, G. W., “Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants”, Proceedings of the National Academy of Sciences of the United States of America, 108: 19641–19646, (2011). DOI: https://doi.org/10.1073/pnas.1104551108
  40. Safaeishakib, M., Assadi, M., and Mehregan, I., Ghazanfar, S., “Phylogenetic study of Silene sections Auriculatae, Spergulifoliae, Ampullatae, and Lasiocalycinae in Iran”, Phytotaxa, 472: 169–183, (2020). DOI: https://doi.org/10.11646/phytotaxa.472.2.7
  41. Safaeishakib, M., Mehregan, I., Ghazanfar, S., and Assadi, M., “Genetic diversity and morphological variability of Iranian Silene aucheriana populations inferred from nrDNA ITS sequences and morphological analysis”, Hacquetia, 23(1), (2024). DOI: https://doi.org/10.2478/hacq-2023-0001
  42. Fassou, G., Korotkova, N, Nersesyan, A., Koch, M. A., Dimopoulos, P., and Borsch, T., “Taxonomy of Dianthus (Caryophyllaceae) – overall phylogenetic relationships and assessment of species diversity based on a first comprehensive checklist of the genus”, PhytoKeys, 196: 91–214, (2022). DOI: https://doi.org/10.3897/phytokeys.196.77940
  43. Nath, S., VanSlambrouck, J. T., Yao, J. W., Gullapalli, A., Razi, F., and Lu, Y., “DNA barcoding of terrestrial invasive plant species in Southwest Michigan”, Plant Direct, 8(6): e615, (2024). DOI: https://doi.org/10.1002/pld3.615
  44. Rautenberg, A., Hathaway, L., Oxelman, B., and Prentice, H. C., “Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences”, Molecular Phylogenetics and Evolution, 57(3): 978–991, (2010). DOI: https://doi.org/10.1016/j.ympev.2010.08.003
  45. Lian, C., Yang, H., Lan, J., Zhang, X., Zhang, F., Yang, J., and Chen, S., “Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens”, PLoS ONE, 17(4): e0266546, (2022). DOI: https://doi.org/10.1371/journal.pone.0266546
  46. Oxelman, B., Lidén, M., and Berglund, D., “Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae)”, Plant Systematics and Evolution, 206: 393–410, (1997). DOI: https://doi.org/10.1007/BF00987959
  47. Zografidis, A., Fragman-Sapir, O., Strid, A., and Dimopoulos, P., “Notes on the generic name Graecobolanthus (Caryophylleae, Caryophyllaceae)” Taxon, 69: 992–997, (2020). DOI: https://doi.org/10.1002/tax.12292
  48. Hoang, T. T., Le, L. B., Le, N. T. K., Nguyen, M. T. A., Truong, A. T. L., Tran, N. T., Tran, V. T., Le, S. V., Duong, K. T., Hoang, K. V. B., Le, T. N., Nguyen, B. V., and Tran, T. V., “Molecular phylogeny and cryptic morphology: A combined approach to taxonomic novelties in Polycarpaea (Caryophyllaceae) from Vietnam”, PLoS One, 19(10): e0301407, (2024). DOI: https://doi.org/10.1371/journal.pone.0301407
  49. Huynh, H. T. T., Cao, T. T. T., Nguyen, C. X., Nguyen, D. T., Nguyen, N. T. B., Cao, D. T. T., Pham, O. T. K., and Nguyen, G. V., “Comparison in DNA barcoding, gene expression and chemical of Pueraria mirifica plants”, The Journal of Animal and Plant Sciences, 34(5): 1303–1316, (2024). DOI: https://doi.org/10.36899/JAPS.2024.5.0812
  50. Doyle, J. J., and Doyle, J. L., “A rapid DNA isolation procedure for small quantities of fresh leaf tissue”, Phytochemical Bulletin, 19: 11–15, (1987).
  51. White, T. J., Bruns, T., Lee, S., and Taylor, J., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., PCR protocols – a guide to methods and applications. San Diego: Academic Press, 315–322, (1990).
  52. Kumar, S., Stecher, G., and Tamura, K., “MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets”, Molecular Biology and Evolution, 33: 1870–1874, (2016). DOI: https://doi.org/10.1093/molbev/msw054
  53. Rambaut, A., “FigTree. Tree figure drawing tool v.1.4.3.”, Available from: http://tree.bio.ed.ac.uk/, (2016).
  54. Ronquist, F., and Huelsenbeck, J. P., “MRBAYES 3: Bayesian phylogenetic inference under mixed models” Bioinformatics, 19: 1572–1574, (2003). DOI: https://doi.org/10.1093/bioinformatics/btg180
  55. Uyanık, M., Kara, Ş. M., and Gürbüz, B., “Importance of biodiversity in terms of sustainable development”, Turkish Journal of Scientific Reviews, (2): 125–127, (2012).