Anadolu Orkidesi’nde (Orchis anatolica Boiss.) Ribozomal DNA’nın Transkripsiyonu Yapılan İç Ara Bölgelerinin (ITS) Özellikleri

Year 2019, , 1117 - 1127, 01.06.2019

Kaan Hürkan

https://doi.org/10.21597/jist.489021

Cited By: 2

Abstract

Orkideler (Orchidaceae), yeryüzünün neredeyse tamamında yayılış gösteren ve çiçekli bitkiler içerisinde en çok tür içeren ikinci familyadır. Bu kalabalık bitki grubunun sınıflandırılması ve filogenetiğinin ortaya çıkarılmasında sadece morfolojiye dayalı yöntemler yetersiz kalmaktadır. Bu çalışmada Orchis anatolica Boiss. türünün çekirdek DNA’sının ITS bölgesi dizilenerek DNA barkodu ortaya çıkarılmış ve bu veri analiz edilerek Pseudorchis albida subsp. straminea (Fernald) Á.Löve & D.Löve, Orchis italica Poir., Orchis anthropophora All., Orchis simia Lam., Orchis purpurea Huds., Orchis militaris Sm., Orchis adenocheila Czerniak, Orchis pallens L., Orchis mascula Crantz, Orchis mascula subsp. pinetorum Boiss. & Kotschy ve Orchis spitzelii Saut. ex W.D.J.Koch türleri ile filogenetik ilişkileri incelenmiştir. Çalışma sonucunda ITS dizisinin tamamının çalışılan Orchis türleri arasında yeterli seviyede ayrım yapabildiği ve bu cins içerisinde yapılacak daha detaylı çalışmalar için kullanılmaya elverişli olduğu sonucuna varılmıştır.

Keywords

Orchidaceae, DNA barkodlama, Transkripsiyonu yapılan iç ara bölgeler (ITS), moleküler filogenetik

Supporting Institution

Çanakkale Onsekiz Mart Üniversitesi Bilimsel Araştırma Projeleri Komisyonu

Project Number

2010/05

Thanks

Çalışmanın gerçekleştirilmesine katkıda bulunan Prof. Dr. Ahmet Gönüz, Prof. Dr. Kemal M. Taşkın, Dr. Öğr. Üyesi Necmettin Güler ve Dr. Fatih Sezer’e, değerli yorumları ile çalışmanın geliştirilmesine katkıda bulunan anonim hakemlere teşekkür ederiz. Bu çalışma Çanakkale Onsekiz Mart Üniversitesi Bilimsel Araştırma Projeleri Komisyonu tarafından 2010/05 numaralı proje ile desteklenmiştir.

Properties of the Internal Transcribed Spacer Region of the Nuclear Ribosomal DNA on Orchis anatolica Boiss.

Abstract

Orchid family (Orchidaceae) is the second largest group of flowering plants and it spreads almost every location in the world. Taxonomic and phylogenetic studies depending only on morphologic characters are not sufficient to discriminate the family. Therefore, in this study we sequenced the whole nuclear ribosomal ITS region and evaluated the discrimination performance of the ITS region on the phylogeny within Pseudorchis albida subsp. straminea (Fernald) Á.Löve & D.Löve, Orchis italica Poir., Orchis anthropophora All., Orchis simia Lam., Orchis purpurea Huds., Orchis militaris Sm., Orchis adenocheila Czerniak, Orchis pallens L., Orchis mascula Crantz, Orchis mascula subsp. pinetorum Boiss. & Kotschy and Orchis spitzelii Saut. ex W.D.J.Koch species. The results of the study showed that the resolution power of the ITS is enough to discriminate studied Orchis spp. at species level.

Keywords

Orchidaceae, Internal Transcribed Spacer (ITS), DNA Barcoding, molecular phylogenetic

Project Number

2010/05

References

• Aceto Caputo P, Cozzolino S, Gaudio L ve Moretti A, 1999. Phylogeny and Evolution of Orchis and Allied Genera Based on ITS DNA Variation: morphological gaps and molecular continuity. Molecular Phylogenetics and Evolution, 13(1), 67–76. doi:10.1006/mpev.1999.0628
• Alvarez-Molina A ve Cameron KM, 2009. Molecular Phylogenetics of Prescottiinae S.L. and Their Close Allies (Orchidaceae, Cranichideae) Inferred From Plastid and Nuclear Ribosomal DNA Sequences. American Journal of Botany, 96(5), 1020–1040. doi:10.3732/ajb.0800219
• Álvarez I, 2003. Ribosomal ITS Sequences and Plant Phylogenetic Inference. Molecular Phylogenetics and Evolution, 29(3), 417–434. doi:10.1016/S1055-7903(03)00208-2
• Bailey C, 2003. Characterization of Angiosperm nrDNA Polymorphism, Paralogy, and Pseudogenes. Molecular Phylogenetics and Evolution, 29(3), 435–455. doi:10.1016/j.ympev.2003.08.021
• Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS ve Donoghue MJ, 1995. The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden, 82(2), 247–277.
• Bateman RM, 2009. Evolutionary Classification of European Orchids: The Crucial Importance of Maximising Explicit Evidence and Minimising Authoritarian Speculation. Journal Europäischer Orchideen, 41(2), 243–318.
• Bateman RM, Hollingsworth PM, Preston J, Yi-Bo L, Pridgeon AM ve Chase MW, 2003. Molecular Phylogenetics and Evolution of Orchidinae and Selected Habenariinae (Orchidaceae). Botanical Journal of the Linnean Society, 142(1), 1–40. doi:10.1046/j.1095-8339.2003.00157.x
• Campbell CS, Wright W, Cox M, Vining TF, Major CS ve Arsenault MP, 2005. Nuclear Ribosomal DNA Internal Transcribed Spacer 1 (ITS1) in Picea (Pinaceae): Sequence Divergence and Structure. Molecular Phylogenetics and Evolution, 35(1), 165–185. doi:10.1016/J.YMPEV.2004.11.010
• Dizkırıcı A, İşler S ve Yiğit O, 2017. Molecular Phylogenetics of Some Orchis Species (Orchidaceae) Native To Turkey Using Nuclear and Chloroplast DNA Sequences. Gazi University Gazi University, 30(2), 35–43.
• Doyle ve Doyle JL, 1987. A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical Bulletin, 19, 15–87. doi:10.2307/4119796
• Feliner GN ve Rosselló JA, 2007. Better the Devil You Know? Guidelines for Insightful Utilization of nrDNA ITS in Species-Level Evolutionary Studies in Plants. Molecular Phylogenetics and Evolution, 44(2), 911–919. doi:10.1016/j.ympev.2007.01.013
• Gulyás G, Sramkó G, Molnár VA, Rudnóy S, Illyés Z, Balázs T, Bratek Z, 2005. Nuclear Ribosomal DNA ITS Paralogs as Evidence of Recent Interspecific Hybridization in The Genus Ophrys (Orchidaceae). Acta Biologica Cracoviensia Series Botanica, 47, 61–67.
• Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Little DP, 2009. A DNA Barcode for Land Plants. Proceedings of the National Academy of Sciences, 106(31), 12794–12797. doi:10.1073/pnas.0905845106
• Hürkan K, 2017. Karasal Bitkilerde DNA Barkodlama: Bazı DNA Barkod Bölgelerinin İncelenmesi. International Journal of Innovative Approaches in Science Research, 1(1), 57–67. doi:10.29329/ijiasr.2017.99.6
• Jin W-T, Schuiteman A, Chase MW, Li J-W, Chung S-W, Hsu T-C ve Jin X-H, 2017. Phylogenetics of Subtribe Orchidinae s.l. (Orchidaceae; Orchidoideae) Based on Seven Markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for Generic Delimitation. BMC Plant Biology, 17(1), 222. doi:10.1186/s12870-017-1160-x
• Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Drummond A, 2012. Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data. Bioinformatics, 28(12), 1647–1649. doi:10.1093/bioinformatics/bts199
• Kreutz CAJ, 2009. Türkiye Orkideleri (Botanik Özellikleri, Ekolojik Özellikleri, Doğal Yayılış Alanları, Yaşam Tehditleri, Koruma Önlemleri). Rota Yayınları, İstanbul-Türkiye. ISBN: 9786054015078
• Kumar S, Stecher G, Li M, Knyaz C ve Tamura K, 2018. MEGA X: Molecular Evolutionary Genetics Analysis Across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547–1549. doi:10.1093/molbev/msy096
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Higgins DG, 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23(21), 2947–2948. doi:10.1093/bioinformatics/btm404
• Mayer, Christoph, Phobos 3.3.11, 2006-2010.
• Pridgeon AM, Bateman RM, Cox A V, Hapeman JR ve Chase MW, 1997. Phylogenetics of Subtribe Orchidinae (Orchidoideae, Orchidaceae) Based on Nuclear ITS Sequences. 1. Intergeneric Relationships and Polyphyly of Orchis sensu lato. Lindleyana, 12(3), 89–109.
• Rudall PJ ve Bateman RM, 2003. Evolutionary Change in Flowers and Inflorescences: Evidence From Naturally Occurring Terata. Trends in Plant Science, 8(2), 76–82. doi:10.1016/S1360-1385(02)00026-2
• Sezik E, 1984. Orkidelerimiz Türkiye’nin Orkideleri. Istanbul-Türkiye. Sandoz Kültür Yayınları.
• Shipunov AB, Fay MF, Pillon Y, Bateman RM ve Chase MW, 2004. Dactylorhiza (Orchidaceae) in European Russia: Combined Molecular and Morphological Analysis. American Journal of Botany, 91(9), 1419–1426.
• Sramko G, Attila M V., Hawkins JA. ve Bateman RM, 2014. Molecular Phylogeny and Evolutionary History of the Eurasiatic Orchid genus Himantoglossum s.l. (Orchidaceae). Annals of Botany, 114(8), 1609–1626. doi:10.1093/aob/mcu179
• Swofford DL, 2003. PAUP*. Phylogenetic Analysis Using Parsimony. Version 4. Sinauer Associates, Sunderland, Massachusetts.
• The Plant List (2013). Published on the Internet; http://www.theplantlist.org/ (Erişim tarihi 10.10.2018).
• White TJ, Bruns TD, Lee S ve Taylor JW, 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. M. A. Innis, D. H. Gelfand, J. J. Sninsky ve T. J. White (Ed.), PCR protocols: A guide to methods and applications içinde (ss. 315–322). San-Diego: Academic Press.
• Won H ve Renner SS, 2005. The Internal Transcribed Spacer of Nuclear Ribosomal DNA in the Gymnosperm Gnetum. Molecular Phylogenetics and Evolution, 36(3), 581–597. doi:10.1016/j.ympev.2005.03.011
• Zimmer EA ve Wen J, 2012. Using Nuclear Gene Data for Plant Phylogenetics: Progress and Prospects. Molecular Phylogenetics and Evolution, 65(2), 774–785. doi:10.1016/j.ympev.2012.07.015