Phylogenetic Analysis of Some Species of the Genus Biarum Based on the Chloroplast trnLC Intron Region

Öz

This study was conducted to reveal the phylogenetic relationships of 12 Biarum species collected from different regions of Turkey based on the chloroplast DNA trnLC intron region. The genus Biarum, belonging to the family Araceae, holds an important place in the flora of Turkey and is represented by 12 taxa in our country. Some of these species are endemic to Turkey, and due to their highly similar morphological structures, molecular-level analyses were needed. In this study, DNA was isolated from the leaves of plant specimens, and the trnLC gene region was amplified by PCR and subsequently sequenced. The sequence data obtained were aligned using the MEGA X software, and a Neighbor-Joining phylogenetic tree was constructed using the Kimura-2 parameter model. According to the findings, it was determined that the genus Biarum generally forms a monophyletic group, and certain species pairs exhibited very close relationships with high bootstrap values (for example, B. x cinarense and B. carduchorum). Similarly, B. bovei and B. crispulum also demonstrated a close evolutionary relationship, while B. eximium, B. syriacum, and B. tenuifolium subsp. zelebori were positioned on the more basal branches of the phylogenetic tree, indicating earlier diverging lineages. Moreover, the molecular findings were largely consistent with the morphological similarities and geographical proximities of the species. It was concluded that the trnLC region is meaningful for the systematics of Biarum species, but it should be supported with additional chloroplast or nuclear markers, especially to distinguish closely related species.

Anahtar Kelimeler

• Flora
• Turkey
• Molecular
• Biarum

Kaynakça

1. Haigh AL, Gibernau M, Maurin O, Bailey P, Carlsen MM, Hay A, et al. Target sequence data shed new light on the infrafamilial classification of Araceae. American Journal of Botany. 2023; 110(2):e16117.
2. Mill RR. Biarum Schott. In Davis PH, editors. Flora of Turkey and the East Aegean Islands. Vol 8. Edinburgh: Edinburgh Univ. Press; 1984. p. 41-63.
3. Alpinar K. Biarum Schott. In Davis PH, editors. Flora of Turkey and the East Aegean Islands (Suppl. 2). Vol 11. Edinburgh: Edinburgh Univ. Press; 2000. p. 221.
4. Akan H, Balos, MM. 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. 2008;32(4):305-310.
5. Boyce PC. A taxonomic revision of Biarum. Curtis's Botanical Magazine. 2008; 25(1):2-17.
6. Yıldırım H, Balos MM, Altıoğlu Y, Akan H. Biarum aleppicum J. Thiébaut (Araceae): Türkiye için yeni bir tür kaydı. Bağbahçe Bilim Dergisi. 2016:3(2);12-19.
7. Yıldırım H, Altıoğlu Y. Biarum rifatii (Araceae): Güneybatı Anadolu'dan yeni bir Yılanpancarı (Biarum Schott.) türü. Bağbahçe Bilim Dergisi. 2016:3(1); 41-46.
8. Yıldırım H. 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. 2018:2;520-541

9. Çeçen C, Akan H, Yıldırım H, Balos, MM. Biarum× cinarense (Araceae), a New Natural Hybrid from SE Turkey. Annales Botanici Fennici. 2022:59(1);67-73. doi: 10.5735/085.059.0112
10. Çeçen C, Akan H, Balos MM. The Synopsis of the Genus Biarum Schott (Araceae) in Türkiye, with Complementary Notes and a Key to the Species. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi. (2025):28(4);955-972.https://doi.org/10.18016/ksutarimdoga.vi.1633070
11. Çeçen C. Türkiye’deki Biarum Schott (Araceae) Cinsinin Taksonomik Revizyonu (Doctoral dissertation). Şanlıurfa: Harran Üniversitesi; 2022.
12. Yeşil Y, İnal İ. Ethnomedicinal Plants of Hasankeyf (Batman-Turkey). Frontiers in Pharmacology. 2021;11:1-19. https://doi.org/10.3389/fphar.2020.624710.
13. Balos MM, Akan H, Durmaz EN, İlgaz FZ Araceae Familyasına Ait Bazı Taksonların Süt Pıhtılaştırma Özelliklerinin Araştırılması. International Journal of Life Sciences and Biotechnology. 2021;43:412-419.
14. Balos, MM, Akan H, Geçit M. Mardin (Türkiye) Geofitleri Üzerine Etnobotanik Bir Araştırma. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi.2022;25(6):1287-1304. https://doi.org/10.18016/ksutarimdoga.vi.976110
15. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA, 2005;102:8369-8374.
16. Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Little DPA DNA barcode for land plants. Proc. Natl. Acad.Sci. USA 106. 2009;12794-12797. [CrossRef]
17. Karapatzak E, Krigas N, Ganopoulos I, Papanastasi K, Kyrkas D, Yfanti P, Nikisianis N, Karydas A, Manthos I, Kosma IS et al. Documenting greek indigenous germplasm of cornelian cherry (Cornus mas L.) for sustainable utilization: Molecular authentication, asexual propagation, and phytochemical evaluation. Plants. 2022;11:1345.
18. Wang J, Fu CN, Mo ZQ, Möller M, Yang JB, Zhang ZR, Li DZ, Gao LM. Testing the complete plastome for species discrimination, cryptic species discovery and phylogenetic resolution in Cephalotaxus (Cephalotaxaceae). Front. Plant Sci. 2022:13;768810.
19. Hollingsworth ML, Andra CA, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM. Selecting barcoding loci for plants: Evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol. Ecol. Resour. 2009: 9;439-457.
20. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madriñán S, Petersen G, Seberg O, Jørgsensen T, Cameron KM, Carine M. et al. A proposal for a standardised protocol to barcode all land plants. Taxon. 2007:56;295-299.
21. Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE. 2007:2;e508.
22. Hollingsworth PM, Graham SW, Little DP. Choosing and using a plant DNA barcode. PLoS ONE. 2011:6;e19254. [CrossRef]
23. Qian ZH, Munywoki JM, Wang QF, Malombe I, Li ZZ, Chen JM. Molecular identification of African Nymphaea species (water lily) based on ITS, trnT-trnF and rpl16. Plants. 2022; 11(18):2431.
24. Zanjanchi P, Mehrvarz SS. The generic position of Loranthus grewingkii of Lorantheae (Loranthaceae) inferred from the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL Intron -F sequences: A case study on Loranthus in Iran. Webbia. 2015;70:199-206. https://doi.org/10.1080/00837792.2015.1064585
25. Sevindik E, Murathan ZT, Filiz S, Yalçin K. Molecular characterization based on chloroplast (trnL Intron -F) DNA sequence of the apple genotypes in Ardahan/Turkey. Bangladesh J Bot. 2019;48 (4):1099-1106. https://doi.org/10.3329/bjb.v48i4.49058
26. Sanna M, Cires E, Pérez-Haase A, Fernández Prieto JA. Haplotype and ribotype diversity of Saxifraga cuneifolia s. l. (Saxifragaceae). Syst Biodivers. 2019;17(4):402-411. https://doi.org/10.1080/14772000.2019.1607614
27. Sevindik E, Okan K. Genetic diversity and phylogenetic analyzes of Laurus nobilis L. (Lauraceae) populations revealed chloroplast (cpDNA) trnL Intron intron and trnL Intron -F region. Intl J Fruit Sci. 2020;20 (S2):82-93. https://doi.org/10.1080/15538362.2019.1707745.
28. Yi Y-J, Zhang J, Xiao X-X, He S. 2021. Delongia flavolimbata (S.He & Y.J.Yi) S.He & Y.J.Yi, an unusual species with elamellate laminae from China, newly combined in Polytrichaceae based on molecular data. J Bryol 43: 313-320. https://doi.org/10.1080/03736687.2021.2004358.
29. Hocaoglu-Ozyigit A, Ucar B, Altay V, Ozyigit II. Genetic diversity and phylogenetic analyses of Turkish cotton (Gossypium hirsutum L.) lines using ISSR markers and chloroplast trnL Intron -F regions. J Nat Fibers. 2022;19:1837-1850. https://doi.org/10.1080/15440478.2020.1788493
30. Chebet D, Musila FM, Kituyi SN, Muthike GM, Kaigongi MM. Molecular phylogeny of selected Kenyan Eucalyptus species inferred from matK, rbcL and trnL Intron -F genes and their suitability for power transmission poles. Diversity. 2022;14(7):563. https://doi.org/10.3390/d14070563.
31. D’yachenko EA, Filyushin MA, Pronina EP, Kochieva EZ. Variability of the trnL Intron plastid gene’s intron in the Faboideae species (Fabaceae). Russ J Genet Appl Res. 2015;5:220-226. https://doi.org/10.1134/S2079059715030053.
32. Hartvig I, Czako M, Kjær ED, Nielsen LR, Theilade I. The use of DNA barcoding in identification and conservation of rosewood (Dalbergia spp.). PLoS ONE. 2015;10 (9):e0138231. https://doi.org/10.1371/journal.pone.0138231.
33. Koohdar F, Sheidai M. Molecular barcoding of Melissa officinalis L. (badranjboye) in Iran and identification of adulteration in its medicinal services. BMC Plant Biol. 2022; 22:587. https://doi.org/10.1186/s12870-022-03957-3
34. Kipkiror N, Muge EK, Ochieno DMW, Nyaboga EN. DNA barcoding markers provide insight into species discrimination, genetic diversity and phylogenetic relationships of yam (Dioscorea spp.). Biologia. 2023;78:689-705. https://doi.org/10.1007/s11756-022-01244-y.
35. Chen CW, Huang YM, Kuo LY, Nguyen QD, Luu HT, Callado JR, Farrar DR, Chiou WL. trnL Intron -F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae). Ann Bot. 2013;111 (4): 663-673. https://doi.org/10.1093/aob/mct004.
36. Taberlet P, Gielly L, Pautou G, Bouvet J. Universal primers for amplification of three noncoding regions of chloroplast DNA. Plant Mol. Biol. 1991;17:1105-1109
37. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution.2018;35:1547-1549. https://doi.org/10.1093/molbev/msy096