Öz
DNA barcoding is an important molecular approach in the determination of species diversity, evaluation of phylogenetic relationships and identification of taxonomically problematic species because of insufficient diagnostic characters. It has great importance to determine the barcoding regions that will give the best result in the evaluation of phylogenetic relationships in species like Trifolium that spread over wide geographical regions in the world and show high variation accordingly. For this aim, matK (maturase K) and rbcL (ribulose bisphosphate carboxylase gene) regions belonging to cpDNA(chloroplast DNA) was used to determine the barcoding ability and evaluate the taxonomy of the genus Trifolium. 63 taxa from matK region and 47 taxa from rbcL region were determined and used in this study. It was observed that transitional substitutions for matK and rbcL regions are higher than transversional substitutions with the rate of 51.52 % and 70.69 %, respectively. It can be stated that both of barcoding regions are valuable to reveal the phylogenetic relationships, in addition to their grouping ability the species as taxonomically. However, especially the using of matK sequence informations that have high variable sites (158) and grouping ability clearly for all taxa is strongly recommended.
Anahtar Kelimeler
Teşekkür
The author would like to thank to NCBI for sequence informations used in this study and the authors sharing the sequence informations in NCBI.
Kaynakça
- Bruni, I., De Mattia, F., Martellos, S., Galimberti, A., Savadori, P., Casiraghi, M., Nimis, PL., & Labra M 2012. DNA Barcoding as an Effective Tool in Improving a Digital Plant Identification System: A Case Study for the Area of Mt. Valerio, Trieste (NE Italy). PLoS ONE 7(9), e43256.
- Burgess, KS., Fazekas, AJ., Kesanakurti, PR., Graham, SW., Husband, BC., Newmaster, SG., Percy, DM., Hajibabaei, M., & Barrett S.C.H 2011. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods in Ecology and Evolution 2, 333-340.
- Choi, I., Ruhlman, TA., & Jansen R.K 2020. Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae. Int J Mol Sci 21(6), 1959.
- de Vere, N., Tim, CGR., Col, RF., Sarah, AT., Charlotte, L., Chris, WM., Danielle, S., Helena, D., Joel, A., Sandra, R., Tatiana, T., Hannah, G., Kevin, W., & Mike J.W 2012. DNA Barcoding the Native Flowering Plants and Conifers of Wales. PLoS ONE 7(6), e37945.
- Elliott, TL., & Davies T.J 2014. Challenges to barcoding an entire flora. Mol Ecol Resour 14(5), 883-91.
- Ellison, NW., Liston, A., Steiner, JJ., Williams, WM., & Taylor N.L 2006. Molecular phylogenetics of the clover genus (Trifolium—Leguminosae). Mol Phylogenet Evol 39(3), 688-705.
- Eroğlu, E., Acar, C., & Turna İ 2013. Homegardens in landscape architecture – a case study of hazelnut plantations. In: Özyavuz, M. (Ed.), Advances in Landscape Architecture. Intech, Zagreb pp. 761-772.
- Gillet, JMX., & Taylor N.L 2001. The World of Clovers. Iowa State University Press, Ames. 457 pp.
- Goldblatt P 1981. Cytology and phylogeny of Leguminosae. In:Polhill RM, Raven PH, editors. Advances in Legume Systematics Part 2. Kew (UK): Royal Botanic Garden. p. 427-463.
- Kajtoch, Ł., Kubisz, D., Heise, W., Mazur, MA., & Babik W 2015. Plant–herbivorous beetle networks: molecular characterization of trophic ecology within a threatened steppic environment. Molecular Ecology 24, 4023-4038.
- Kalinkina, VA., Yulia, VM., & Dmitry E.K 2020. Diversity and taxonomy of the Trifolium lupinaster polymorphic complex in Eastern Europe and Asia. Flora 267, 151597.
- Kıran, Y., Şahin, A., Türkoğlu, I., Kursat, M., & Emre I 2010. Karyology of seven Trifolium L. taxa growing in Turkey. Acta Biologica Cracoviensia Series Botanica 52(2), 81-85.
- Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura K 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35, 1547-1549.
- Kuzmina, ML., Thomas, WAB., Aron, JF., Sean, WG., Stephanie, LD., Anuar, R., Bruce, AB., Timothy, AD., Jeffery, MS., Paul, MC., Steven, GN., Diana, MP., Erin, F., Aurélien, LM., Bruce, F., Lynn, G., Ragupathy, S., Jeannette, W., Linda, J., Deborah, M., Connor, PW., Allison, B., Elizabeth, S., Jeremy, RD., Evgeny, VZ., & Paul D.N.H 2017. Using Herbarium-Derived DNAs to Assemble a Large-Scale DNA Barcode Library for the Vascular Plants of Canada. Applications in Plant Sciences 5(12), 1700079.
- Manton E.R 2016. DNA barcoding the vascular plant flora of Southern British Columbia. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the faculty of graduate and postdoctoral studies. The University of British Columbia.
- NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank.
- Schaefer, H., Olivier, JH., Luı´s, S., Timothy, GB., & Vincent S 2011. Testing Darwin’s naturalization hypothesis in the Azores. Ecology Letters 14, 389-396.
- Thornhill, AH., Bruce, GB., William, AF., Sonia, N., Matthew, MK., Naia, MH., Thomas, PM., David, DA., & Brent D.M 2017. Spatial phylogenetics of the native California flora. BMC Biology 15, 96.
- Uslu E 2012. Karyology of nine Trifolium L. taxa from Turkey. Caryologia 65(4), 304-310.
- Uslu, E., Ertuğrul, GD., & Babaç M.T 2013. Assessment of genetic diversity in naturally growing 29 Trifolium L. taxa from Bolu Province using RAPD and SSR markers. Turk J Biol 37, 479-490.
- Uslu, E., & Babaç M.T 2019. A descriptive study of some Trifolium L. (Clover) taxa grown in Bolu Province. Turk J Bot 43, 673-686.
- Vizintin, L., Javornik, B., & Bohanec B 2006. Genetic characterization of selected Trifolium species as revealed by nuclear DNA content and ITS rDNA region analysis. Plant Sci 170(4), 859-866.
- Watson, LE., Sayed-Ahmed, H., & Badr A 2000. Molecular phylogeny of Old World Trifolium (Fabaceae), based on plastid and nuclear markers. Plant Syst Evol 224, 153-171.
- Zohary, M., & Heller D 1984. The Genus Trifolium. The Israel Academy of Science and Humanities, Jerusalem
Öz
DNA barkodlama; tür çeşitliliğinin tayininde, filogenetik ilişkilerin değerlendirilmesinde ve yetersiz ayırt edici karakterlerden dolayı taksonomik açıdan problemli türlerin kimliklendirilmesinde önemli bir moleküler yaklaşımdır. Geniş coğrafik bölgelere yayılan ve buna bağlı yüksek varyasyon gösteren Trifolium gibi türlerde, filogenetik ilişkilerin değerlendirilmesinde en iyi sonucu verecek barkodlama bölgelerini tayin etmek büyük bir öneme sahiptir. Bu amaçla, cpDNA’ya (chloroplast DNA) ait matK (maturase K) ve rbcL (ribulose bisphosphate carboxylase gen) bölgeleri Trifolium cinsinin taksonomisini değerlendirmek ve barkodlama yeteneğini tayin etmek için kullanıldı. Bu çalışmada matK bölgesinden 63 taxa ve rbcL bölgesinden 47 taxa belirlendi ve kullanıldı. Transisyonel değişimlerin, matK ve rbcL bölgeleri için transversiyonel değişimlerden sırasıyla % 51.52 ve % 70.69 ile daha yüksek olduğu gözlemlendi. Heriki barkodlama bölgesinin taksonomik olarak türleri gruplama yeteneklerinin yanısıra, filogenetik ilişkileri ortaya çıkarmak adına değerli olduğu ifade edilebilir. Bununla birlikte, özellikle bütün taksonlar için açık bir şekilde gruplama yeteneğine ve yüksek oranda değişken bölgelere sahip (158) matK sekans bilgilerinin kullanımı tavsiye edilir.
Anahtar Kelimeler
Kaynakça
- Bruni, I., De Mattia, F., Martellos, S., Galimberti, A., Savadori, P., Casiraghi, M., Nimis, PL., & Labra M 2012. DNA Barcoding as an Effective Tool in Improving a Digital Plant Identification System: A Case Study for the Area of Mt. Valerio, Trieste (NE Italy). PLoS ONE 7(9), e43256.
- Burgess, KS., Fazekas, AJ., Kesanakurti, PR., Graham, SW., Husband, BC., Newmaster, SG., Percy, DM., Hajibabaei, M., & Barrett S.C.H 2011. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods in Ecology and Evolution 2, 333-340.
- Choi, I., Ruhlman, TA., & Jansen R.K 2020. Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae. Int J Mol Sci 21(6), 1959.
- de Vere, N., Tim, CGR., Col, RF., Sarah, AT., Charlotte, L., Chris, WM., Danielle, S., Helena, D., Joel, A., Sandra, R., Tatiana, T., Hannah, G., Kevin, W., & Mike J.W 2012. DNA Barcoding the Native Flowering Plants and Conifers of Wales. PLoS ONE 7(6), e37945.
- Elliott, TL., & Davies T.J 2014. Challenges to barcoding an entire flora. Mol Ecol Resour 14(5), 883-91.
- Ellison, NW., Liston, A., Steiner, JJ., Williams, WM., & Taylor N.L 2006. Molecular phylogenetics of the clover genus (Trifolium—Leguminosae). Mol Phylogenet Evol 39(3), 688-705.
- Eroğlu, E., Acar, C., & Turna İ 2013. Homegardens in landscape architecture – a case study of hazelnut plantations. In: Özyavuz, M. (Ed.), Advances in Landscape Architecture. Intech, Zagreb pp. 761-772.
- Gillet, JMX., & Taylor N.L 2001. The World of Clovers. Iowa State University Press, Ames. 457 pp.
- Goldblatt P 1981. Cytology and phylogeny of Leguminosae. In:Polhill RM, Raven PH, editors. Advances in Legume Systematics Part 2. Kew (UK): Royal Botanic Garden. p. 427-463.
- Kajtoch, Ł., Kubisz, D., Heise, W., Mazur, MA., & Babik W 2015. Plant–herbivorous beetle networks: molecular characterization of trophic ecology within a threatened steppic environment. Molecular Ecology 24, 4023-4038.
- Kalinkina, VA., Yulia, VM., & Dmitry E.K 2020. Diversity and taxonomy of the Trifolium lupinaster polymorphic complex in Eastern Europe and Asia. Flora 267, 151597.
- Kıran, Y., Şahin, A., Türkoğlu, I., Kursat, M., & Emre I 2010. Karyology of seven Trifolium L. taxa growing in Turkey. Acta Biologica Cracoviensia Series Botanica 52(2), 81-85.
- Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura K 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35, 1547-1549.
- Kuzmina, ML., Thomas, WAB., Aron, JF., Sean, WG., Stephanie, LD., Anuar, R., Bruce, AB., Timothy, AD., Jeffery, MS., Paul, MC., Steven, GN., Diana, MP., Erin, F., Aurélien, LM., Bruce, F., Lynn, G., Ragupathy, S., Jeannette, W., Linda, J., Deborah, M., Connor, PW., Allison, B., Elizabeth, S., Jeremy, RD., Evgeny, VZ., & Paul D.N.H 2017. Using Herbarium-Derived DNAs to Assemble a Large-Scale DNA Barcode Library for the Vascular Plants of Canada. Applications in Plant Sciences 5(12), 1700079.
- Manton E.R 2016. DNA barcoding the vascular plant flora of Southern British Columbia. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the faculty of graduate and postdoctoral studies. The University of British Columbia.
- NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank.
- Schaefer, H., Olivier, JH., Luı´s, S., Timothy, GB., & Vincent S 2011. Testing Darwin’s naturalization hypothesis in the Azores. Ecology Letters 14, 389-396.
- Thornhill, AH., Bruce, GB., William, AF., Sonia, N., Matthew, MK., Naia, MH., Thomas, PM., David, DA., & Brent D.M 2017. Spatial phylogenetics of the native California flora. BMC Biology 15, 96.
- Uslu E 2012. Karyology of nine Trifolium L. taxa from Turkey. Caryologia 65(4), 304-310.
- Uslu, E., Ertuğrul, GD., & Babaç M.T 2013. Assessment of genetic diversity in naturally growing 29 Trifolium L. taxa from Bolu Province using RAPD and SSR markers. Turk J Biol 37, 479-490.
- Uslu, E., & Babaç M.T 2019. A descriptive study of some Trifolium L. (Clover) taxa grown in Bolu Province. Turk J Bot 43, 673-686.
- Vizintin, L., Javornik, B., & Bohanec B 2006. Genetic characterization of selected Trifolium species as revealed by nuclear DNA content and ITS rDNA region analysis. Plant Sci 170(4), 859-866.
- Watson, LE., Sayed-Ahmed, H., & Badr A 2000. Molecular phylogeny of Old World Trifolium (Fabaceae), based on plastid and nuclear markers. Plant Syst Evol 224, 153-171.
- Zohary, M., & Heller D 1984. The Genus Trifolium. The Israel Academy of Science and Humanities, Jerusalem
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Yapısal Biyoloji |
| Bölüm | ARAŞTIRMA MAKALESİ (Research Article) |
| Yazarlar | |
| Yayımlanma Tarihi | 30 Nisan 2023 |
| Gönderilme Tarihi | 29 Mart 2022 |
| Kabul Tarihi | 14 Ağustos 2022 |
| Yayımlandığı Sayı | Yıl 2023 |
2022-JIF = 0.500
2022-JCI = 0.170
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