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Preliminary Insights into the Phylogeny of Colchicum Species

Yıl 2024, Cilt: 27 Sayı: Ek Sayı 2 (Suppl 2), 350 - 360
https://doi.org/10.18016/ksutarimdoga.vi.1518459

Öz

Colchicum has played a vital role in the field of medicine due to its inherent properties, with its importance extending from the past to the present. DNA barcoding is an effective tool for the identification and conservation of plant species. This study tested the application of the 18S rRNA gene for the phylogenetic construction of Colchicum species. The phylogenetic UPGMA (unweighted pair group method with arithmetic mean) tree and STRUCTURE analysis were conducted to assess the consistency of the results for 33 Colchicum specimens and one outgroup species, utilizing the 18S rRNA partial gene. The results of the study showed that DNA barcoding using 18S rRNA was an effective method for identifying Colchicum species, with 97.76% of the tested sequences being successfully determined. This study contributes to the field of phylogenetic analysis of Colchicum species by illustrating the utility of the 18S rRNA gene for phylogenetic construction, underscoring its significance in advancing our understanding of plant genetics. The nucleotide sequences obtained for species identification in this study were uploaded to the barcode of life data system (BOLD), contributing to internationally accessible genetic data.

Teşekkür

I would like to express my gratitude to Prof. Ahu ALTINKUT UNCUOĞLU from the Department of Bioengineering at Marmara University and Prof. Yıldız AYDIN from the Department of Biology at Marmara University for their significant contributions to the completion of this study.

Kaynakça

  • Aykut, Y. (2020). The importance in DNA barcoding of the regions which is covering rRNA genes and its sequences in the genus Quercus L. Bangladesh Journal of Plant Taxonomy, 27(2), 261-271.
  • Chandra, L.D. (2016). Bio-diversity and conservation of medicinal and aromatic plants. Advances in Plants & Agriculture Research, 5(4), 00186.
  • Bae, Y. M. (2009). DNA sequencing and phylogenetic analysis of the 18s rRNA gene of Atractylodes japonica Koidz and analysis of atractylon. Korean Journal of Medicinal Crop Science, 17(1), 26-32.
  • Demirel, F., Gürcan, K., & Akar, T. (2022). Molecular characterization and assessment of population structure of hulled wheats. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, 25(1), 192-199.
  • Dong, T.T., Ma, X.Q., Clarke, C., Song, Z.H., Ji, Z.N., et al. (2003). Phylogeny of Astragalus in China: molecular evidence from the DNA sequences of 5S rRNA spacer, ITS, and 18S rRNA. Journal of Agricultural and Food Chemistry, 51(23), 6709-6714.
  • Doyle, J.J., & Doyle, J.L. (1987). A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bulletin, 19(1), 11-15.
  • Düşen, O.D., & Sümbül, H. (2007). A morphological investigation of Colchicum L.(Liliaceae) species in the Mediterranean region in Turkey. Turkish Journal of Botany, 31(5), 373-419.
  • Earl, D.A., VonHoldt, B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359-361.
  • Eckenrode, V.K., Arnold, J., Meagher, R.B. (1985). Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs. Journal of Molecular Evolution, 21, 259-269.
  • Evanno, G., Regnaut, S., Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620.
  • Fukunaga, K., Hill, J., Vigouroux, Y., Matsuoka, Y., Sanchez, G.J., Liu, K., Buckler, E.S., Doebley, J. (2005). Genetic diversity and population structure of teosinte. Genetics, 169(4), 2241-2254.
  • Gandhi, Y., Rawat, H., Kumar, V., Thakur, A., Mishra, S. K., Charde, V., ... & Acharya, R. (2023). Identification of two kinds of Colchicum corms by DNA barcoding, physicochemical, chromatographic and chemometric analyses along with pharmacognostic parameters. Microchemical Journal, 195, 109399.
  • Hailu, T., Sharma, R., Mann, S., Gupta, P., Gupta, R. K., Rani, A. (2021). Determination of bioactive phytochemicals, antioxidant and anti-inflammatory activity of Colchicum autumnale L.(Suranjanshireen). Indian Journal of Natural Products and Resources (IJNPR)[Formerly Natural Product Radiance (NPR)], 12(1), 52-60.
  • Hamby, R.K., & Zimmer, E.A. (1988). Ribosomal RNA sequences for inferring phylogeny within the grass family (Poaceae). Plant Systematics and Evolution, 160, 29-37.
  • Hebert, P.D., Cywinska, A., Ball, S.L., DeWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), 313-321.
  • Hollingsworth, P.M., Graham, S.W., Little, D.P. (2011). Choosing and using a plant DNA barcode. PloS One, 6(5), e19254.
  • Karakan, F.Y., Kiliç, A., & Çetin, B.E. (2024). Altınözü ilçesinde yetiştirilen sarımsak (Allium sativum L.) genotiplerinin morfolojik ve moleküler karakterizasyonu. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, 27(2), 333-343.
  • Karakas, O.M., Turktas, M., Ertugrul, F., Kaya, E. (2014). Use of fluorescent-based amplified fragment length polymorphism to resolve phylogenetic relationships of Colchicum species from Turkey. Genetics and Molecular Research, 13(1), 1480-1490.
  • Kress, W.J. (2017). Plant DNA barcodes: Applications today and in the future. Journal of Systematics and Evolution, 55(4), 291-307.
  • Kress, W.J., & Erickson, D.L. (2008). DNA barcoding: A windfall for tropical biology?. Biotropica 40 (4): 405-408.
  • Messing, J., Carlson, J., Hagen, G., Rubenstein, I., Oleson, A. (1984). Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region. DNA, 3(1), 31-40.
  • Mishra, P., Kumar, A., Nagireddy, A., Mani, D.N., Shukla, A.K., Tiwari, R., Sundaresan, V. (2016). DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnology Journal, 14(1), 8-21.
  • Nickrent, D.L., & Soltis, D.E. (1995). A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Annals of the Missouri Botanical Garden, 82(2), 208-234.
  • Persson, K., Petersen, G., del Hoyo, A., Seberg, O., Jørgensen, T. (2011). A phylogenetic analysis of the genus Colchicum L. (Colchicaceae) based on sequences from six plastid regions. Taxon, 60(5), 1349-1365.
  • Pritchard, J.K., Stephens, M., Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
  • Rather, R.A., Bano, H., Firoz, A., Mohammed Ali, H., Bhat, M.A., Padder, S.A., Nafees, H., Hakeem, K.R. (2022). The assessment of morphological diversity of Colchicum luteum L., an economically important threatened medicinal plant of Kashmir Himalaya. Sustainability, 14(3), 1327.
  • Safhi, F.A., ALshamrani, S.M., Jalal, A.S., El-Moneim, D.A., Alyamani, A.A., Ibrahim, A.A. (2022). Genetic characterization of some Saudi Arabia’s accessions from commiphora gileadensis using physio-biochemical parameters, molecular markers, DNA barcoding analysis and relative gene expression. Genes, 13(11), 2099.
  • Sahin, E.C., Mete, S., Aydemir, M., Aydin, Y., Uncuoglu, A.A. (2020). Assessing Pylogenetic Accuracy of Plant Species with Chloroplast and Nuclear Genome Specific Markers. In F. Vardar, Y. Aydin, A.A. Uncuoglu (Eds), Recent Advances in Plant Science, (pp. 33-63). Nova Science Publishers,Inc.
  • Sahin, E.C., Kaya, E., Tuyel, U., Aydin, Y, Ozhatay, N., Uncuoglu, A.A. (2021). An assessment on the floristic variety of Colchicum genus of Turkey in terms of morphological characteristics. Scientia Horticulturae, 287, 110251.
  • Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K., Lane, R. (2005). Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1805-1811.
  • Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.J., Hoot, S.B., Sweere, J.A., Kuzoff, R.K., Kron, K.A., Chase, M.W., Swensen, S.M., Zimmer, E.A., Chaw, S.M., Gillespie, L.J., Kress, W.J., Sytsma, K.J. (1997). Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Annals of the Missouri Botanical Garden, 84(1), 1–49.
  • Soltis, D. E., Soltis, P. S., Chase, M. W., Mort, M. E., Albach, D. C., Zanis, M., ... & Farris, J. S. (2000). Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society, 133(4), 381-461.
  • Srivastava, S., Sanchita, Bhargava, M., Sharma, A. (2016). DNA Barcoding of Medicinal Plants. In H.S. Tsay, L.F. Shyur, D. Agrawal, Y.C. Wu, S.Y. Wang (Eds.), Medicinal Plants - Recent Advances in Research and Development. Springer, Singapore.
  • Takaiwa, F., Oono, K., Sugiura, M. (1984). The complete nucleotide sequence of a rice 17S rRNA gene. Nucleic Acids Research, 12(13), 5441-5448.
  • Techen, N., Parveen, I., Pan, Z., Khan, I.A. (2014). DNA barcoding of medicinal plant material for identification. Current Opinion in Biotechnology, 25, 103-110.
  • Toplan, G.G., Gürer, Ç., Mat, A. (2016). Importance of Colchicum species in modern therapy and its significance in Turkey. Journal of Faculty of Pharmacy of Istanbul University, 46(2), 129-144.
  • Tüyel, A.U., Şahin, E.Ç., Akfirat, F.Ş., Aydin, Y., Uncuoğlu, A.A. (2020). Phylogenetic analysis of Colchicum (Colchicaceae) genus by molecular markers from nuclear and chloroplast genome. Genetics & Applications, 4(1), 1-11.
  • Yang, Y. W., Lai, K. N., Tai, P. Y., Ma, D. P., & Li, W. H. (1999). Molecular phylogenetic studies of Brassica, Rorippa, Arabidopsis and allied genera based on the internal transcribed spacer region of 18S–25S rDNA. Molecular Phylogenetics and Evolution, 13(3), 455-462.

Colchicum Türlerinin Filogenisine İlişkin Ön Bilgiler

Yıl 2024, Cilt: 27 Sayı: Ek Sayı 2 (Suppl 2), 350 - 360
https://doi.org/10.18016/ksutarimdoga.vi.1518459

Öz

Colchicum, sahip olduğu doğal özellikleri nedeniyle tıp alanında önemli bir rol oynamış olup, önemi geçmişten günümüze kadar uzanmaktadır. DNA barkodlama, bitki türlerinin tanımlanması ve korunması için etkili bir araçtır. Bu çalışma, Colchicum türlerinin filogenetik yapısının oluşturulmasında 18S rRNA geninin uygulamasını test etmiştir. 33 Colchicum örneği ve bir dış grup türü kullanılarak, 18S rRNA kısmi geni ile filogenetik UPGMA (aritmetik ortalama ile ağırlıksız çift grup yöntemi) ağacı ve STRUCTURE analizi yapılmıştır. Çalışmanın sonuçları, 18S rRNA kullanılarak yapılan DNA barkodlamanın Colchicum türlerinin tanımlanmasında etkili bir yöntem olduğunu ve test edilen dizilerin %97.76'sının başarılı bir şekilde belirlendiğini göstermiştir. Bu çalışma, 18S rRNA geninin filogenetik yapı oluşturmadaki faydasını göstererek Colchicum türlerinin filogenetik analizine katkıda bulunmakta ve bitki genetiğini anlama konusunda ilerlememize olanak sağlamaktadır. Tür tanımlaması için elde edilen nükleotid dizileri, uluslararası erişilebilir genetik verilere katkıda bulunmak amacıyla yaşam barkodu veri sistemine (BOLD) yüklenmiştir.

Teşekkür

Bu çalışmanın tamamlanmasındaki önemli katkılarından dolayı, Marmara Üniversitesi Biyomühendislik Bölümü'nden Prof. Ahu ALTINKUT UNCUOĞLU'na ve Marmara Üniversitesi Biyoloji Bölümü'nden Prof. Yıldız AYDIN'a teşekkürlerimi sunuyorum.

Kaynakça

  • Aykut, Y. (2020). The importance in DNA barcoding of the regions which is covering rRNA genes and its sequences in the genus Quercus L. Bangladesh Journal of Plant Taxonomy, 27(2), 261-271.
  • Chandra, L.D. (2016). Bio-diversity and conservation of medicinal and aromatic plants. Advances in Plants & Agriculture Research, 5(4), 00186.
  • Bae, Y. M. (2009). DNA sequencing and phylogenetic analysis of the 18s rRNA gene of Atractylodes japonica Koidz and analysis of atractylon. Korean Journal of Medicinal Crop Science, 17(1), 26-32.
  • Demirel, F., Gürcan, K., & Akar, T. (2022). Molecular characterization and assessment of population structure of hulled wheats. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, 25(1), 192-199.
  • Dong, T.T., Ma, X.Q., Clarke, C., Song, Z.H., Ji, Z.N., et al. (2003). Phylogeny of Astragalus in China: molecular evidence from the DNA sequences of 5S rRNA spacer, ITS, and 18S rRNA. Journal of Agricultural and Food Chemistry, 51(23), 6709-6714.
  • Doyle, J.J., & Doyle, J.L. (1987). A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bulletin, 19(1), 11-15.
  • Düşen, O.D., & Sümbül, H. (2007). A morphological investigation of Colchicum L.(Liliaceae) species in the Mediterranean region in Turkey. Turkish Journal of Botany, 31(5), 373-419.
  • Earl, D.A., VonHoldt, B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359-361.
  • Eckenrode, V.K., Arnold, J., Meagher, R.B. (1985). Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs. Journal of Molecular Evolution, 21, 259-269.
  • Evanno, G., Regnaut, S., Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620.
  • Fukunaga, K., Hill, J., Vigouroux, Y., Matsuoka, Y., Sanchez, G.J., Liu, K., Buckler, E.S., Doebley, J. (2005). Genetic diversity and population structure of teosinte. Genetics, 169(4), 2241-2254.
  • Gandhi, Y., Rawat, H., Kumar, V., Thakur, A., Mishra, S. K., Charde, V., ... & Acharya, R. (2023). Identification of two kinds of Colchicum corms by DNA barcoding, physicochemical, chromatographic and chemometric analyses along with pharmacognostic parameters. Microchemical Journal, 195, 109399.
  • Hailu, T., Sharma, R., Mann, S., Gupta, P., Gupta, R. K., Rani, A. (2021). Determination of bioactive phytochemicals, antioxidant and anti-inflammatory activity of Colchicum autumnale L.(Suranjanshireen). Indian Journal of Natural Products and Resources (IJNPR)[Formerly Natural Product Radiance (NPR)], 12(1), 52-60.
  • Hamby, R.K., & Zimmer, E.A. (1988). Ribosomal RNA sequences for inferring phylogeny within the grass family (Poaceae). Plant Systematics and Evolution, 160, 29-37.
  • Hebert, P.D., Cywinska, A., Ball, S.L., DeWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), 313-321.
  • Hollingsworth, P.M., Graham, S.W., Little, D.P. (2011). Choosing and using a plant DNA barcode. PloS One, 6(5), e19254.
  • Karakan, F.Y., Kiliç, A., & Çetin, B.E. (2024). Altınözü ilçesinde yetiştirilen sarımsak (Allium sativum L.) genotiplerinin morfolojik ve moleküler karakterizasyonu. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, 27(2), 333-343.
  • Karakas, O.M., Turktas, M., Ertugrul, F., Kaya, E. (2014). Use of fluorescent-based amplified fragment length polymorphism to resolve phylogenetic relationships of Colchicum species from Turkey. Genetics and Molecular Research, 13(1), 1480-1490.
  • Kress, W.J. (2017). Plant DNA barcodes: Applications today and in the future. Journal of Systematics and Evolution, 55(4), 291-307.
  • Kress, W.J., & Erickson, D.L. (2008). DNA barcoding: A windfall for tropical biology?. Biotropica 40 (4): 405-408.
  • Messing, J., Carlson, J., Hagen, G., Rubenstein, I., Oleson, A. (1984). Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region. DNA, 3(1), 31-40.
  • Mishra, P., Kumar, A., Nagireddy, A., Mani, D.N., Shukla, A.K., Tiwari, R., Sundaresan, V. (2016). DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnology Journal, 14(1), 8-21.
  • Nickrent, D.L., & Soltis, D.E. (1995). A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Annals of the Missouri Botanical Garden, 82(2), 208-234.
  • Persson, K., Petersen, G., del Hoyo, A., Seberg, O., Jørgensen, T. (2011). A phylogenetic analysis of the genus Colchicum L. (Colchicaceae) based on sequences from six plastid regions. Taxon, 60(5), 1349-1365.
  • Pritchard, J.K., Stephens, M., Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
  • Rather, R.A., Bano, H., Firoz, A., Mohammed Ali, H., Bhat, M.A., Padder, S.A., Nafees, H., Hakeem, K.R. (2022). The assessment of morphological diversity of Colchicum luteum L., an economically important threatened medicinal plant of Kashmir Himalaya. Sustainability, 14(3), 1327.
  • Safhi, F.A., ALshamrani, S.M., Jalal, A.S., El-Moneim, D.A., Alyamani, A.A., Ibrahim, A.A. (2022). Genetic characterization of some Saudi Arabia’s accessions from commiphora gileadensis using physio-biochemical parameters, molecular markers, DNA barcoding analysis and relative gene expression. Genes, 13(11), 2099.
  • Sahin, E.C., Mete, S., Aydemir, M., Aydin, Y., Uncuoglu, A.A. (2020). Assessing Pylogenetic Accuracy of Plant Species with Chloroplast and Nuclear Genome Specific Markers. In F. Vardar, Y. Aydin, A.A. Uncuoglu (Eds), Recent Advances in Plant Science, (pp. 33-63). Nova Science Publishers,Inc.
  • Sahin, E.C., Kaya, E., Tuyel, U., Aydin, Y, Ozhatay, N., Uncuoglu, A.A. (2021). An assessment on the floristic variety of Colchicum genus of Turkey in terms of morphological characteristics. Scientia Horticulturae, 287, 110251.
  • Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K., Lane, R. (2005). Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1805-1811.
  • Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.J., Hoot, S.B., Sweere, J.A., Kuzoff, R.K., Kron, K.A., Chase, M.W., Swensen, S.M., Zimmer, E.A., Chaw, S.M., Gillespie, L.J., Kress, W.J., Sytsma, K.J. (1997). Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Annals of the Missouri Botanical Garden, 84(1), 1–49.
  • Soltis, D. E., Soltis, P. S., Chase, M. W., Mort, M. E., Albach, D. C., Zanis, M., ... & Farris, J. S. (2000). Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society, 133(4), 381-461.
  • Srivastava, S., Sanchita, Bhargava, M., Sharma, A. (2016). DNA Barcoding of Medicinal Plants. In H.S. Tsay, L.F. Shyur, D. Agrawal, Y.C. Wu, S.Y. Wang (Eds.), Medicinal Plants - Recent Advances in Research and Development. Springer, Singapore.
  • Takaiwa, F., Oono, K., Sugiura, M. (1984). The complete nucleotide sequence of a rice 17S rRNA gene. Nucleic Acids Research, 12(13), 5441-5448.
  • Techen, N., Parveen, I., Pan, Z., Khan, I.A. (2014). DNA barcoding of medicinal plant material for identification. Current Opinion in Biotechnology, 25, 103-110.
  • Toplan, G.G., Gürer, Ç., Mat, A. (2016). Importance of Colchicum species in modern therapy and its significance in Turkey. Journal of Faculty of Pharmacy of Istanbul University, 46(2), 129-144.
  • Tüyel, A.U., Şahin, E.Ç., Akfirat, F.Ş., Aydin, Y., Uncuoğlu, A.A. (2020). Phylogenetic analysis of Colchicum (Colchicaceae) genus by molecular markers from nuclear and chloroplast genome. Genetics & Applications, 4(1), 1-11.
  • Yang, Y. W., Lai, K. N., Tai, P. Y., Ma, D. P., & Li, W. H. (1999). Molecular phylogenetic studies of Brassica, Rorippa, Arabidopsis and allied genera based on the internal transcribed spacer region of 18S–25S rDNA. Molecular Phylogenetics and Evolution, 13(3), 455-462.
Toplam 38 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Bitki Biyoteknolojisi
Bölüm ARAŞTIRMA MAKALESİ (Research Article)
Yazarlar

Ezgi Çabuk Şahin 0000-0003-1505-5752

Erken Görünüm Tarihi 19 Aralık 2024
Yayımlanma Tarihi
Gönderilme Tarihi 18 Temmuz 2024
Kabul Tarihi 12 Ekim 2024
Yayımlandığı Sayı Yıl 2024Cilt: 27 Sayı: Ek Sayı 2 (Suppl 2)

Kaynak Göster

APA Çabuk Şahin, E. (2024). Preliminary Insights into the Phylogeny of Colchicum Species. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 27(Ek Sayı 2 (Suppl 2), 350-360. https://doi.org/10.18016/ksutarimdoga.vi.1518459

21082



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