Research Article
Defining phylogenetic relationship between the genera Opopanax and Crenosciadium using nuclear and chloroplast DNA sequence data
Abstract
A phylogenetic study of the Opopanax and Crenosciadium was conducted to elucidate their circumscription and infrageneric relationships. Sequence data from nrDNA ITS, cpDNA matK and trnL-F were used to determine their phylogenetic relationship. Polymerase Chain Reaction (PCR) amplifications of all regions were performed using universal primers. Maximum Likelihood (ML) trees were constructed using PAUP* software, another phylogenetic tree of ITS sequences showing node ages was obtained from MrBayes programme and Neighbour Net Diagrams were constructed using Splits Tree programme. Our results clearly showed that Smyrniopsis and Opopanax are allied strongly with Petroedmondia syriaca, Magydaris panacifolia, and Crenosciadium siifolium.
Keywords
Supporting Institution
Selçuk Üniversitesi
Project Number
17401082
Thanks
We express our thanks to the Scientific Investigation Projects Coordinate Office of the Selçuk University (Project number: 17401082) for financial support.
References
- Pimenov, M.G., Leonov, M.V., The genera of the Umbelliferae, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, (1993).
- Amiri, M.S., Joharchi, M.R., Ethnobotanical knowledge of Apiaceae family in Iran: A review, Avicenna Journal of Phytomedicine, 6, 6 621–635, (2016).
- Menglan, S., Fading, P., Zehui, P., Watson, M.F., Cannon, J.F.M., Holmes-Smith, I., Kljuykov, E.V., Phillippe, L.R., Pimenov, M.G., Apiaceae (Umbelliferae). In: Flora of China. Ed. Wu Zhengyi, R. H. Raven Vol. 14 (Apiaceae through Ericaceae), Missouri Botanical garden Press, Beijing: Science Press & St. Louis, 1–205, (2005).
- Guner, A., Aslan, S., Ekim, T., Vural, M., Babaç, M.T. (Eds.), Türkiye Bitkileri Listesi (Damarlı Bitkiler), Nezahat Gökyigit Botanik Bahçesi ve Flora Arastirma Dernegi Yayını, Istanbul, (2012).
- Rechinger, K.H., Trinia In: Rechinger, K.H. & Hedge, I.C. (eds.), Flora Iranica 162, Akademische Druck and Verlagsanstalt, Graz, Austria, 343-344, (1987).
- Meikle, R.D. (Ed.), Flora of Cyprus, vol 1. Bentham-Moxon Trust and Royal Botanic Garden, Kew, 757–758, (1977)
- Shishkin, B.K., Opopanax, Flora of the U.S.S.R. Volume 17 (Umbelliflorae). Botanical Institute of the Academy of Sciences of the USSR, Moscow-Leningrad, (1973).
- Tutin, T.G., Opopanax L. In: Tutin, T.G., Heywood, V.H., Burges, N.A., Moore, D.M., Valentine, D.H., Walters, S.M. & Webb, D.A. (Eds.) Flora Europaea, vol. 2., Cambridge University Press, Cambridge, 360, (1968).
- Chamberlain, D.F., Opopanax Koch. In: Davis, P.H. (Ed.) Flora of Turkey and the East Aegean Island, vol. 4., Edinburgh University Press, Edinburgh, 471–473, (1972).
- Çetin, Ö., Çelik, M., Comparative morphological, anatomical, micromorphological, and palynological studies on the genera Opopanax and Crenosciadium (Apiaceae), Phytotaxa, 372, 1, 35–50, (2018).
- Katz-Downie, D.S., Valiejo-Roman, C.M., Terentieva, E.I., Troitsky, A.V., Pimenov, M.G., Lee, B., Downie, S.R., Towards a molecular phylogeny of Apiaceae subfamily Apioideae: additional information from nuclear ribosomal DNA ITS sequences, Plant Systematics and Evolution, 216, 167–195, (1999).
- Ajani, Y., Ajani, A., Cordes, J.M., Watson, M.F., Downie, S.R., Phylogenetic analysis of nrDNA ITS sequences reveals relationships within five groups of Iranian Apiaceae subfamily Apioideae, Taxon, 57, 383–401, (2008).
- White, T.J. Bruns, T., Lee, S., Taylor, J., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, In: PCR Protocols: A Guide to Methods and Applications, Innis, M.A. et. al. (eds), Academic Press, Inc., New York, 315-322, (1990).
- Sang, T., Crawford, DJ., Stuessy TF., Mario Silva O., ITS sequences and the phylogeny of the genus Robinsonia (Asteraceae), Systematic Botany, 20, 55–64, (1995).
- Taberlet, P., Gielly, L., Pautou, G., Bouvet J., Universal primers for amplification of three noncoding regions of chloroplast DNA, Plant Molecular Biology, 17, 1105–1109, (1991).
- CBOL Plant Working Group, A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106, 31, 12794–12797, (2009). Swofford, D.L., PAUP: phylogenetic analysis using parsimony, version 4.0 b10. Sinauer Associates, Sunderland MA, (2002).
- Altekar, G., Dwarkadas, S., Huelsenbeck, J.P., Ronquist, F., Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics, 20, 407–415, (2004).
- De Candolle, A.P., Umbelliferae. In A.P. de Candolle [ed.], Prodromus systematis naturalis regni vegetabilis, 4: 55–250, (1830).
- Bentham, G., Umbelliferae. In Bentham G & Hooker J. D. [eds.], Genera Plantarum, 1, 859–931, Reeve, London, UK, (1867).
- Downie, S.R., Spalik, K., Katz-Downie, D.S., Reduron, J.P., Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences, Evolution and Biodiversity of Plants, 128, 111–136, (2010).
- Drude, C.G.O., Umbelliferae. In Engler A. and Prantl K. [eds.], Die naturlichen Pflanzenfamilien, 3, 63–250, Wilhelm Engelmann, Leipzig, Germany, (1897-1898).
- Sprengel C.P.J., Umbelliferae. In J. J. Roemer and J. A. Schultes [eds.], Systema Vegetabilium, 6, xxix–lx, 315–628, (1820).
- Koch, W.D.J., Generum tribuum queplantarum Umbelliferarum nova dispositio. Nova Acta Academiae Caesareae Leopoldino–Carolinae Germanicae Naturae Curiosorum, 12, 55–156, (1824).
- Downie, S.R., Katz-Downie, D.S., Watson, M.F., A phylogeny of the flowering plant family apiaceae based on chloroplast dna rpl16 and rpoc1 intron sequences: towards a suprageneric classification of subfamily Apioideae, American Journal of Botany, 87, 2, 273–292, (2000).
- Shneyer, V.S., Borschtschenko, G.P., Pimenov, M.G., Leonov, M.V., The tribe Smyrnieae (Umbelliferae) in the light of serotaxonomical analysis, Plant Systematics and Evolution, 182, 135–148, (1992).
- Downie, S.R., Katz-Downie, S., A molecular phylogeny of Apiaceae subfamily Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences, American Journal of Botany, 83, 234–251, (1996).
- Plunkett, D., Soltis E., Soltis P.S., Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences, American Journal of Botany, 83, 499–515, (1996).
- Downie, S.R., Ramanath, S., Katz-Downie, D.S., Ilanas, E., Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid rpoC1 intron sequences, American Journal of Botany, 85, 563–591, (1998).
- Valiejo-Roman, C.M., Pimenov M.G., Terentieva E.I., Downie S.R., Katz-Downie D.S., Troitsky A.V., Molecular systematics of the Umbelliferae: using nuclear rDNA internal transcribed spacer sequences to resolve issues of evolutionary relationships, Botanicheskii Zhurnal, 83, 1–22, (1998).
- Tamamschian, S.G., Grammosciadium DC. In: Rechinger KH (ed.). Flora Iranica Vol. 162, 96–100, Akademische Drucku, Verlagsanalt, Graz, (1987).
- Menemen, Y., Opopanax In Güner, A., et. al. (eds.) Türkiye Bitkileri Listesi (Damarlı Bitkiler), Neazahat Gökyiğit Botanik Bahçesi ve Flora Araştırma Derneği Yayını, İstanbul, (2012).
- Plunkett, G.M., Downie, S.R., Major lineages within Apiaceae subfamily Apioideae: a comparison of chloroplast restriction site and DNA sequence data, American Journal of Botany, 86, 1014–1026, (1999).
- Spalik, K., Downie, S.R., Intercontinental disjunctions in Cryptotaenia (Apiaceae, Oenantheae): an appraisal using molecular data, Journal of Biogeography, 34, 2039–2054, (2007).
- Koch, M.A., Bani, B., German, D.A., Huang, X.C., Phylogenetics, phylogeography and vicariance of polyphyletic Grammosciadium (Apiaceae: Careae) in Anatolia, Botanical Journal of the Linnean Society, 185, 168–188, (2017).
- Magee, A.R., van Wyk, B.-E., Tilney, P.M., Downie, S.R., Generic delimitations and relationships of the Cape genera Capnophyllum, Dasispermum and Sonderina, the North African genera Krubera and Stoibrax, and a new monotypic genus of the subfamily Apioideae (Apiaceae), Systematic Botany, 34, 580–594, (2009).
- Winter, P.J.D., Magee, A.R., Phephu, N., Tilney, P.M., Downie, S.R., van Wyk, B.E., A new generic classification for African peucedanoid species (Apiaceae), Taxon, 57, 347–364, (2008).
- Boissier, E., Flora Orientalis, vol. 2, Geneva, Switzerland, H. Georg, (1872).
Opopanax ve Crenosciadium cinsleri arasındaki filogenetik ilişkinin çekirdek ve kloroplast DNA dizisi verilerinin kullanılarak belirlenmesi
Abstract
Opopanax ve Crenosciadium üzerine filogenetik bir çalışma, cinslerin sınırlarını ve cinsler arası ilişkilerini aydınlatmak için yapıldı. Çekirdek DNA’sından ITS, kloroplast DNA’sından matK ve trnL-F'’den elde edilen dizi verileri, filogenetik ilişkilerini belirlemek için kullanıldı. Tüm bölgelerin Polimeraz Zincir Reaksiyonu (PCR) amplifikasyonları evrensel primerler kullanılarak yapıldı. Maksimum Olabilirlik (ML) ağaçları, PAUP* yazılımı kullanılarak oluşturuldu, ITS dizilerinin nod yaşlarını gösteren bir diğer filogenetik ağacı MrBayes programından elde edildi ve Komşu Ağ Diyagramları, Splits Tree Programı kullanılarak oluşturuldu. Sonuçlarımız, Smyrniopsis ve Opopanax'ın Petroedmondia syriaca, Magydaris panacifolia ve Crenosciadium siifolium ile güçlü bir şekilde yakın ilişkili olduğunu açıkça gösterdi.
Keywords
Project Number
17401082
References
- Pimenov, M.G., Leonov, M.V., The genera of the Umbelliferae, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, (1993).
- Amiri, M.S., Joharchi, M.R., Ethnobotanical knowledge of Apiaceae family in Iran: A review, Avicenna Journal of Phytomedicine, 6, 6 621–635, (2016).
- Menglan, S., Fading, P., Zehui, P., Watson, M.F., Cannon, J.F.M., Holmes-Smith, I., Kljuykov, E.V., Phillippe, L.R., Pimenov, M.G., Apiaceae (Umbelliferae). In: Flora of China. Ed. Wu Zhengyi, R. H. Raven Vol. 14 (Apiaceae through Ericaceae), Missouri Botanical garden Press, Beijing: Science Press & St. Louis, 1–205, (2005).
- Guner, A., Aslan, S., Ekim, T., Vural, M., Babaç, M.T. (Eds.), Türkiye Bitkileri Listesi (Damarlı Bitkiler), Nezahat Gökyigit Botanik Bahçesi ve Flora Arastirma Dernegi Yayını, Istanbul, (2012).
- Rechinger, K.H., Trinia In: Rechinger, K.H. & Hedge, I.C. (eds.), Flora Iranica 162, Akademische Druck and Verlagsanstalt, Graz, Austria, 343-344, (1987).
- Meikle, R.D. (Ed.), Flora of Cyprus, vol 1. Bentham-Moxon Trust and Royal Botanic Garden, Kew, 757–758, (1977)
- Shishkin, B.K., Opopanax, Flora of the U.S.S.R. Volume 17 (Umbelliflorae). Botanical Institute of the Academy of Sciences of the USSR, Moscow-Leningrad, (1973).
- Tutin, T.G., Opopanax L. In: Tutin, T.G., Heywood, V.H., Burges, N.A., Moore, D.M., Valentine, D.H., Walters, S.M. & Webb, D.A. (Eds.) Flora Europaea, vol. 2., Cambridge University Press, Cambridge, 360, (1968).
- Chamberlain, D.F., Opopanax Koch. In: Davis, P.H. (Ed.) Flora of Turkey and the East Aegean Island, vol. 4., Edinburgh University Press, Edinburgh, 471–473, (1972).
- Çetin, Ö., Çelik, M., Comparative morphological, anatomical, micromorphological, and palynological studies on the genera Opopanax and Crenosciadium (Apiaceae), Phytotaxa, 372, 1, 35–50, (2018).
- Katz-Downie, D.S., Valiejo-Roman, C.M., Terentieva, E.I., Troitsky, A.V., Pimenov, M.G., Lee, B., Downie, S.R., Towards a molecular phylogeny of Apiaceae subfamily Apioideae: additional information from nuclear ribosomal DNA ITS sequences, Plant Systematics and Evolution, 216, 167–195, (1999).
- Ajani, Y., Ajani, A., Cordes, J.M., Watson, M.F., Downie, S.R., Phylogenetic analysis of nrDNA ITS sequences reveals relationships within five groups of Iranian Apiaceae subfamily Apioideae, Taxon, 57, 383–401, (2008).
- White, T.J. Bruns, T., Lee, S., Taylor, J., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, In: PCR Protocols: A Guide to Methods and Applications, Innis, M.A. et. al. (eds), Academic Press, Inc., New York, 315-322, (1990).
- Sang, T., Crawford, DJ., Stuessy TF., Mario Silva O., ITS sequences and the phylogeny of the genus Robinsonia (Asteraceae), Systematic Botany, 20, 55–64, (1995).
- Taberlet, P., Gielly, L., Pautou, G., Bouvet J., Universal primers for amplification of three noncoding regions of chloroplast DNA, Plant Molecular Biology, 17, 1105–1109, (1991).
- CBOL Plant Working Group, A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106, 31, 12794–12797, (2009). Swofford, D.L., PAUP: phylogenetic analysis using parsimony, version 4.0 b10. Sinauer Associates, Sunderland MA, (2002).
- Altekar, G., Dwarkadas, S., Huelsenbeck, J.P., Ronquist, F., Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics, 20, 407–415, (2004).
- De Candolle, A.P., Umbelliferae. In A.P. de Candolle [ed.], Prodromus systematis naturalis regni vegetabilis, 4: 55–250, (1830).
- Bentham, G., Umbelliferae. In Bentham G & Hooker J. D. [eds.], Genera Plantarum, 1, 859–931, Reeve, London, UK, (1867).
- Downie, S.R., Spalik, K., Katz-Downie, D.S., Reduron, J.P., Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences, Evolution and Biodiversity of Plants, 128, 111–136, (2010).
- Drude, C.G.O., Umbelliferae. In Engler A. and Prantl K. [eds.], Die naturlichen Pflanzenfamilien, 3, 63–250, Wilhelm Engelmann, Leipzig, Germany, (1897-1898).
- Sprengel C.P.J., Umbelliferae. In J. J. Roemer and J. A. Schultes [eds.], Systema Vegetabilium, 6, xxix–lx, 315–628, (1820).
- Koch, W.D.J., Generum tribuum queplantarum Umbelliferarum nova dispositio. Nova Acta Academiae Caesareae Leopoldino–Carolinae Germanicae Naturae Curiosorum, 12, 55–156, (1824).
- Downie, S.R., Katz-Downie, D.S., Watson, M.F., A phylogeny of the flowering plant family apiaceae based on chloroplast dna rpl16 and rpoc1 intron sequences: towards a suprageneric classification of subfamily Apioideae, American Journal of Botany, 87, 2, 273–292, (2000).
- Shneyer, V.S., Borschtschenko, G.P., Pimenov, M.G., Leonov, M.V., The tribe Smyrnieae (Umbelliferae) in the light of serotaxonomical analysis, Plant Systematics and Evolution, 182, 135–148, (1992).
- Downie, S.R., Katz-Downie, S., A molecular phylogeny of Apiaceae subfamily Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences, American Journal of Botany, 83, 234–251, (1996).
- Plunkett, D., Soltis E., Soltis P.S., Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences, American Journal of Botany, 83, 499–515, (1996).
- Downie, S.R., Ramanath, S., Katz-Downie, D.S., Ilanas, E., Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid rpoC1 intron sequences, American Journal of Botany, 85, 563–591, (1998).
- Valiejo-Roman, C.M., Pimenov M.G., Terentieva E.I., Downie S.R., Katz-Downie D.S., Troitsky A.V., Molecular systematics of the Umbelliferae: using nuclear rDNA internal transcribed spacer sequences to resolve issues of evolutionary relationships, Botanicheskii Zhurnal, 83, 1–22, (1998).
- Tamamschian, S.G., Grammosciadium DC. In: Rechinger KH (ed.). Flora Iranica Vol. 162, 96–100, Akademische Drucku, Verlagsanalt, Graz, (1987).
- Menemen, Y., Opopanax In Güner, A., et. al. (eds.) Türkiye Bitkileri Listesi (Damarlı Bitkiler), Neazahat Gökyiğit Botanik Bahçesi ve Flora Araştırma Derneği Yayını, İstanbul, (2012).
- Plunkett, G.M., Downie, S.R., Major lineages within Apiaceae subfamily Apioideae: a comparison of chloroplast restriction site and DNA sequence data, American Journal of Botany, 86, 1014–1026, (1999).
- Spalik, K., Downie, S.R., Intercontinental disjunctions in Cryptotaenia (Apiaceae, Oenantheae): an appraisal using molecular data, Journal of Biogeography, 34, 2039–2054, (2007).
- Koch, M.A., Bani, B., German, D.A., Huang, X.C., Phylogenetics, phylogeography and vicariance of polyphyletic Grammosciadium (Apiaceae: Careae) in Anatolia, Botanical Journal of the Linnean Society, 185, 168–188, (2017).
- Magee, A.R., van Wyk, B.-E., Tilney, P.M., Downie, S.R., Generic delimitations and relationships of the Cape genera Capnophyllum, Dasispermum and Sonderina, the North African genera Krubera and Stoibrax, and a new monotypic genus of the subfamily Apioideae (Apiaceae), Systematic Botany, 34, 580–594, (2009).
- Winter, P.J.D., Magee, A.R., Phephu, N., Tilney, P.M., Downie, S.R., van Wyk, B.E., A new generic classification for African peucedanoid species (Apiaceae), Taxon, 57, 347–364, (2008).
- Boissier, E., Flora Orientalis, vol. 2, Geneva, Switzerland, H. Georg, (1872).
There are 37 citations in total.
Details
| Primary Language | English |
|---|---|
| Journal Section | Research Articles |
| Authors | |
| Project Number | 17401082 |
| Publication Date | July 4, 2021 |
| Submission Date | October 16, 2020 |
| Published in Issue | Year 2021 Volume: 23 Issue: 2 |