Türkiye’deki Biarum Cinsine Ait Bazı Türlerin Plastid rps16 DNA dizilerine dayalı Filogenetik Analizi

Abstract

DNA’sında bulunan rps16 bölgesine dayalı dizi analizlerini tespit etmek amacıyla yapılmıştır. Metod: Türkiye’nin farklı lokalitelerinde doğal yayılış gösteren 8 Biarum türü toplanarak DNA izolasyonu kit kullanılarak gerçekleştirilmiş ve Polimeraz Zincir Reaksiyonu (PCR) ile rps16 bölgesi çoğaltılmıştır. DNA dizileri analiz edilerek türler arasındaki genetik mesafeler hesaplanmış ve Neighbor-Joining yöntemi kullanılarak filogenetik ağaç oluşturulmuştur. Bulgular: Analizler sonucunda, Biarum bovei ve B. crispulum türlerinin en yakın genetik akraba olarak belirlenirken, Biarum davisii subsp. marmarisense ve B. bovei en uzak akraba türler olarak tespit edilmiştir. Elde edilen genetik analiz sonuçlarının, morfolojik verilere dayalı sınıflandırmayı doğrulamakta ve Biarum türlerinin filogenetik yapısının genetik analizlerle desteklenmesi gerektiğini ortaya koymaktadır. Sonuç: İlk defa bu çalışma ile Biarum cinsine ait genetik veriler elde edilmiş olup gelecekte, coğrafi ve ekolojik faktörlerin de dahil olduğu daha kapsamlı markörlerin de kullanılarak filogenetik çalışmaların yapılması önerilmektedir.

Keywords

• Kloroplast DNA
• rps16
• filogenetik
• Biarum

Project Number

Harran University (project no. BAP-20055)

Ethical Statement

Acknowledgement: We would like to thank Harran University and TUBITAK- Scientist Support Programs Directorate (BIDEP) for their financial support in this study. Conflicts of interest: No Conflict of Interest. Funding: Harran University (project no. BAP-20055) and TÜBİTAK-Scientist Support Programs Directorate (BİDEP) supported as financially. Ethical statement: This study does not require ethical approval. Author contributions: All authors contributed to the study conception and design. All authors read and approved the final manuscript.

Phylogenetic analysis of some species of the Biarum genus in Turkey based on plastid rps16 DNA sequences

Abstract

Purpose: In this study, phylogenetic relationships of some species of Biarum genus naturally distributed in Turkey were determined by sequence analyses based on rps16 region in chloroplast DNA. Method: 8 Biarum species naturally distributed in different localities of Turkey were collected and DNA isolation was performed using a kit, and rps16 region was amplified by Polymerase Chain Reaction (PCR). Genetic distances between species were calculated by analyzing DNA sequences and a phylogenetic tree was constructed using the Neighbor-Joining method. Findings: As a result of the analyses, Biarum bovei and B. crispulum species were identified as the closest genetic relatives, while Biarum davisii subsp. marmarisense and B. bovei were determined as the most distant relatives. The obtained genetic analysis results confirm the classification based on morphological data and reveal that the phylogenetic structure of Biarum species should be supported by genetic analyses. Conclusion: This study provides one of the first phylogenetic analyses based on the rps16 chloroplast region in Turkish Biarum species and it is recommended that future phylogenetic studies be conducted using more comprehensive markers including geographical and ecological factors.

Keywords

• Chloroplast DNA
• rps16
• phylogenetics
• Biarum

Supporting Institution

Harran University (project no. BAP-20055) and TUBITAK- Scientist Support Programs Directorate (BIDEP)

Project Number

Harran University (project no. BAP-20055)

Ethical Statement

no ethical statment

Thanks

We would like to thank Harran University (project no. BAP-20055) and TUBITAK- Scientist Support Programs Directorate (BIDEP) for their financial support in this study.

References

1. [1] Boyce, PC. (2008). A taxonomic revision of Biarum. Curtis's botanical magazine, 25(1), 2-17.
2. [2] Mill, R.R. (1984). Biarum in Davis, P.H. (ed.), Flora of Turkey and the East Aegean Islands. Edinburgh, 8, 41–63.
3. [3] Alpınar, K. (2000). Biarum Schott in Davis PH (ed.), Flora of Turkey and the East Aegean Islands (Suppl. 2). Vol 11: 221, Edinburgh: Edinburgh Univ. Press
4. [4] Akan, H. ve Balos, M.M. (2008). Check-list of the genus Biarum Schott in the Flora of Turkey, with a new record for Turkey: Biarum syriacum (Spreng.) H. Riedl. Turkish Journal of Botany, 32(4), 305-310.
5. [5] Yıldırım, H., Balos, M. M., Altıoğlu, Y. and Akan, H. (2016). Biarum aleppicum J. Thiébaut (Araceae): Türkiye için yeni bir tür kaydı. Bağbahçe Bilim Dergisi, 3(2), 12-19.
6. [6] Yıldırım, H. and Altıoğlu, Y. (2016). Biarum rifatii (Araceae): Güneybatı Anadolu'dan yeni bir Yılanpancarı (Biarum Schott.) türü. Bağbahçe Bilim Dergisi, 3(1), 41-46.
7. [7] Yıldırım, H. (2018). Biarum Schott. Şu Eserde: Güner A, Kandemir, A, Menemen, Y, Yıldırım, H, Aslan, S, Ekşi, G, Güner, I. & Çimen, AÖ (edlr.). Resimli Türkiye Florası. ANG Vakfı Nezahat Gökyiğit Botanik Bahçesi Yayınları. İstanbul. 2, 520-541
8. [8] Çeçen, C., Akan, H., Yıldırım, H. and Balos, M.M. (2022). Biarum× cinarense (Araceae), a New Natural Hybrid from SE Turkey. Annales Botanici Fennici, 59(1), 67-73. doi: 10.5735/085.059.0112

9. [9] Yeşil, Y. and İnal, İ. (2021). Ethnomedicinal Plants of Hasankeyf (Batman-Turkey). Front Pharmacol, 11, 1–19. https://doi.org/10.3389/fphar.2020.624710.
10. [10 ] Schott , H. W. (1860). Prodromus systematis aroidearum. Congregationis Mechitharisticae, Vienna, Austria.
11. [11] Engler, A. (1920). Araceae, Pars generalis et index familiae generalis. In A. Engler [ed.], Das Pfl anzenreich 74 (IV.23A), 1 – 71.
12. [12] Grayum, MH. (1990). Evolution and phylogeny of the Araceae. Annals of the Missouri Botanical Garden, 77, 628.
13. [13] Mayo , S.J. Bogner, , J. and Boyce, PC. (1997). The genera of Araceae. Royal Botanic Gardens, Kew, UK.
14. [14] Govaerts , R. , D. G. Frodin , J. Bogner , J. Boos , P. Boyce , B. Cosgriff, T. B. Croat , et al . (2002). World checklist and bibliography of Araceae and Acoraceae. Royal Botanic Gardens, Kew, UK.
15. [15] Agarwal M, Shrivastava N and Padh H (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep, 2, :617–631.
16. [16] Palaz EB, Demirel F, Adali S et al (2023) Genetic relationships of salep orchid species and gene flow among Serapias vomeracea × anacamptis morio hybrids. Plant Biotechnol Rep, 17, 315–327. doi:10.1007/s11816-022-00782-w
17. [17] Karakaya O, Yaman M, Balta F, Yilmaz M, Balta MF (2023). Assessment of genetic diversity revealed by morphological traits and ISSR markers in hazelnut germplasm (Corylus avellana L.) from Eastern Black Sea Region, Turkey. Genet Resour Crop Evol, 70(2), 525–537.
18. [18] Burke, S. V., Grennan, C. P., and Duvall, M. R. (2012). Plastome sequences of two New World bamboos–Arundinaria gigantea and Cryptochloa strictiflora (Poaceae)–extend phylogenomic understanding of Bambusoideae. Am. J. Bot., 99, 1951–1961. doi: 10.3732/ajb.1200365.
19. [19] Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, D. E., and Burleigh, J. G. (2014). From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol. Biol. 14, 23. doi: 10.1186/1471-2148-14-23.
20. [20] Yang, Z., Wang, G., Ma, Q., Ma, W., Liang, L., and Zhao, T. (2019). The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography. PeerJ 7, e6320. doi: 10.7717/peerj.6320
21. [21] Lan, Z., Shi, Y., Yin, Q., Gao, R., Liu, C., Wang, W., ... and Wu, L. (2022). Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species. Frontiers in Plant Science, 13, 1049209. doi: 10.3389/fpls.2022.1049209
22. [22] Wariss, H. M., Yi, T. S., Wang, H., and Zhang, R. (2018). The chloroplast genome of a rare and an endangered species Salweenia bouffordiana (Leguminosae) in China. Conserv. Genet. Resour., 10, 405–407. doi: 10.1007/s12686-017-0836-8
23. [23] Oxelman, B., Lidén, M., and Berglund, D. (1997). Chloroplast rps 16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant systematics and Evolution, 206, 393-410.
24. [24] 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, 1547-1549. https://doi.org/10.1093/molbev/msy096
25. [25] Çeçen, C., Akan, H., Balos, MM (2025). The synopsis of the genus Biarum Schott (Araceae) in Türkiye, with complementary notes and a key to the species. KSÜ Tarım ve Doğa Dergisi, 28 (4), 955-972. doi: 10.18016/ ksutarimdoga. vi.1633070.