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Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae)

Year 2021, Volume: 27 Issue: 1, 69 - 75, 04.03.2021
https://doi.org/10.15832/ankutbd.615848

Abstract

Internal Transcribed Spacer (ITS) is one of the most used barcoding regions for the molecular phylogenetics and barcoding of orchids. Our aim in this study is to test the reliability of ITS on barcoding of closely related Neotinea spp., including Neotinea tridentata, Neotinea ustulata subsp. ustulata and Neotinea ustulata subsp. aestivalis, by comparing it to the accD-psaI intergenic spacer of the plastid DNA. Both ITS and accD-psaI regions were amplified by specific primer sets and sequenced. Phylogenetic trees were regenerated by using Maximum Parsimony approach. The results showed that ITS separated some N. tridentata samples of Turkish, Greek, Hungarian and Croatian samples from the others on the phylogenetic trees due to the incomplete lineage sorting. In contrast to ITS, the accD-psaI marker could successfully separate N. tridentata and N. ustulata samples according to a priori species classification. Our findings refer to a hybridisation story between some N. tridentata and N. ustulata. We propose not to use ITS sequences directly as a barcode and to reconstruct the phylogeny of the Neotinea group. Instead, the inclusion of other nuclear regions such as LFY, ADH, etc., or utilisation of whole genome sequencing could give better barcoding results.

Supporting Institution

Çanakkale Onsekiz Mart University, Scientific Research Coordination Unit

Project Number

BAP FBA-2015-415

Thanks

We are grateful to Dr. Gábor Sramkó for sharing his Neotinea spp. collection. Also, we thank anonymous reviewers who helped to improve the manuscript and Cathy Seither for language proofing. This study has been financially supported by Çanakkale Onsekiz Mart University, Scientific Research Coordination Unit; Project number: BAP FBA-2015-415. This study is based on the Doctoral Thesis titled “Studies on Phylogenetic Analysis of Neotinea ustulata and Neotinea tridentata (Orchidaceae)” written by Kaan Hürkan.

References

  • Álvarez, I., Wendel, J.F. (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 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: 435–455. doi: 10.1016/j.ympev.2003.08.021
  • Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S. & Donoghue, M.J. (1995) The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden 82: 247–277.
  • Bateman, R.M., Hollingsworth, P.M., Preston, J., YI-BO, L., Pridgeon, A.M. & Chase, M.W. (2003) Molecular phylogenetics and evolution of Orchidinae and selected Habenariinae (Orchidaceae). Botanical Journal of the Linnean Society 142: 1–40. doi: 10.1046/j.1095-8339.2003.00157.x
  • Chase, M.W., Fay, M.F. & Savolainen, V. (2000) Higher-level classification in the angiosperms: new insights from the perspective of DNA sequence data. Taxon 49: 685–704.
  • Nieto-Feliner, G.N. & Rosselló, J.A. (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: 911–919. doi: 10.1016/j.ympev.2007.01.013
  • Fuertes Aguilar, J. & Nieto-Feliner, G. (2003) Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae). Molecular Phylogenetics and Evolution 28: 430–447. doi: 10.1016/S1055-7903(02)00301-9
  • Gulyás, G., Sramkó, G., Molnár, V.A. & et al. (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, P.M. (2008) DNA barcoding plants in biodiversity hot spots: progress and outstanding questions. Heredity (Edinb) 101: 1–2. doi: 10.1038/hdy.2008.16
  • Hollingsworth, P.M., Graham, S.W. & Little, D.P. (2011) Choosing and Using a Plant DNA Barcode. PLoS One 6:e19254. doi: 10.1371/journal.pone.0019254
  • Kearse, M., Moir, R., Wilson, A. & et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. doi: 10.1093/bioinformatics/bts199
  • Kim, S.T. & Donoghue, M.J. (2008) Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). American Journal of Botany 95: 1122–35. doi: 10.3732/ajb.0700008
  • Larkin, M.A., Blackshields, G., Brown, N.P. & et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948. doi: 10.1093/bioinformatics/btm404Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y. & Chen, S. (2015) Plant DNA barcoding: from gene to genome. Biological Reviews 90: 157–166. doi: 10.1111/brv.12104
  • Liao, D. (2008) Concerted Evolution. In: John Wiley & Sons Ltd. Encyclopedia of Life Sciences. Chichester, UK, pp. 1–5.
  • Mayol, M. & Rosselló, J.A. (2001) Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus. Molecular Phylogenetics and Evolution 19: 167–176. doi: 10.1006/mpev.2001.0934
  • Pillon, Y., Fay, M.F., Hedrén, M., Bateman, R.M., Devey, D.S., Shipunov, A.B., van der Bank, M., Chase, M.W. & Hedren, M. (2007) Evolution and temporal diversification of western European polyploid species complexes in Dactylorhiza (Orchidaceae). Taxon 56: 1185–1208
  • Pridgeon, A.M., Bateman, R.M., Cox, A.V., Hapeman, J.R. & Chase, M.W. (1997) Phylogenetics of subtribe Orchidinae (Orchidoideae, Orchidaceae) based on nuclear ITS sequences. 1. Intergeneric relationships and polyphyly of Orchis sensu lato. Lindleyana 12: 89–109.
  • Rieseberg, L.H. (1997) Hybrid origins of plant species. Annual Review of Ecology, Evolution, and Systematics 28: 359–389.
  • Rieseberg, L.H., Whitton, J. & Linder, C.R. (1996) Molecular marker incongruence in plant hybrid zones and phylogenetic trees. Acta Botanica Neerlandica 45: 243–262.
  • Shipunov, A.B., Fay, M.F., Pillon, Y., Bateman, R.M. & Chase, M.W. (2004) Dactylorhiza (Orchidaceae) in European Russia: Combined molecular and morphological analysis. American Journal of Botany 91: 1419–1426.
  • Small, R.L., Ryburn, J.A., Cronn, R.C., Seelanan, T. & Wendel, J.F. (1998) The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301–1315.
  • Sramkó, G. (2008) Sequence variability of the nrITS in the Ophrys fuciflora species-complex of the Mediterranean bee-orchid (Ophrys L.) genus. Department of Botany. University of Debrecen, Debrecen.
  • Sramko, G., Attila, M.V., Hawkins, J.A. & Bateman, R.M .(2014) Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). Annals of Botany 114: 1609–1626. doi: 10.1093/aob/mcu179
  • Sramkó, G., Gulyás, G., Matus, G., Rudnóy, S., Illyés, Z., Bratek, Z. & Molnár, A. (2008) Leaf width, nrDNA and cpDNA its sequence variation within central European Bulbocodium vernum and B. versicolor (Colchicaceae) populations: Are there really two taxa? Acta Biologica Academiae Scientiarum Hungaricae 59: 103–114.
  • Sramkó, G., Molnár, V.A., Hawkins, J.A. & Bateman, R.M. (2011) Evolution of the Eurasiatic genus Himantoglossum(Orchideae, Orchidoideae): an integrativephylogenetic approach. In: In: Abstracts of the XVIII International Botanical Congress. Comittee of the XVIII IBC 2011, Melbourne, pp. 286–287.
  • Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
  • White, T.J., Bruns, T.D., Lee, S. & Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (Eds.) PCR protocols: A guide to methods and applications. Academic Press, San-Diego, pp. 315–322.
  • Won, H. & Renner, S.S. (2005) The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Molecular Phylogenetics and Evolution 36: 581–597. doi: 10.1016/j.ympev.2005.03.011
  • Zimmer, E.A. & Wen, J. (2012) Using nuclear gene data for plant phylogenetics: Progress and prospects. Molecular Phylogenetics and Evolution 65: 774–785. doi: 10.1016/j.ympev.2012.07.015
Year 2021, Volume: 27 Issue: 1, 69 - 75, 04.03.2021
https://doi.org/10.15832/ankutbd.615848

Abstract

Project Number

BAP FBA-2015-415

References

  • Álvarez, I., Wendel, J.F. (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 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: 435–455. doi: 10.1016/j.ympev.2003.08.021
  • Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S. & Donoghue, M.J. (1995) The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden 82: 247–277.
  • Bateman, R.M., Hollingsworth, P.M., Preston, J., YI-BO, L., Pridgeon, A.M. & Chase, M.W. (2003) Molecular phylogenetics and evolution of Orchidinae and selected Habenariinae (Orchidaceae). Botanical Journal of the Linnean Society 142: 1–40. doi: 10.1046/j.1095-8339.2003.00157.x
  • Chase, M.W., Fay, M.F. & Savolainen, V. (2000) Higher-level classification in the angiosperms: new insights from the perspective of DNA sequence data. Taxon 49: 685–704.
  • Nieto-Feliner, G.N. & Rosselló, J.A. (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: 911–919. doi: 10.1016/j.ympev.2007.01.013
  • Fuertes Aguilar, J. & Nieto-Feliner, G. (2003) Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae). Molecular Phylogenetics and Evolution 28: 430–447. doi: 10.1016/S1055-7903(02)00301-9
  • Gulyás, G., Sramkó, G., Molnár, V.A. & et al. (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, P.M. (2008) DNA barcoding plants in biodiversity hot spots: progress and outstanding questions. Heredity (Edinb) 101: 1–2. doi: 10.1038/hdy.2008.16
  • Hollingsworth, P.M., Graham, S.W. & Little, D.P. (2011) Choosing and Using a Plant DNA Barcode. PLoS One 6:e19254. doi: 10.1371/journal.pone.0019254
  • Kearse, M., Moir, R., Wilson, A. & et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. doi: 10.1093/bioinformatics/bts199
  • Kim, S.T. & Donoghue, M.J. (2008) Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). American Journal of Botany 95: 1122–35. doi: 10.3732/ajb.0700008
  • Larkin, M.A., Blackshields, G., Brown, N.P. & et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948. doi: 10.1093/bioinformatics/btm404Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y. & Chen, S. (2015) Plant DNA barcoding: from gene to genome. Biological Reviews 90: 157–166. doi: 10.1111/brv.12104
  • Liao, D. (2008) Concerted Evolution. In: John Wiley & Sons Ltd. Encyclopedia of Life Sciences. Chichester, UK, pp. 1–5.
  • Mayol, M. & Rosselló, J.A. (2001) Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus. Molecular Phylogenetics and Evolution 19: 167–176. doi: 10.1006/mpev.2001.0934
  • Pillon, Y., Fay, M.F., Hedrén, M., Bateman, R.M., Devey, D.S., Shipunov, A.B., van der Bank, M., Chase, M.W. & Hedren, M. (2007) Evolution and temporal diversification of western European polyploid species complexes in Dactylorhiza (Orchidaceae). Taxon 56: 1185–1208
  • Pridgeon, A.M., Bateman, R.M., Cox, A.V., Hapeman, J.R. & Chase, M.W. (1997) Phylogenetics of subtribe Orchidinae (Orchidoideae, Orchidaceae) based on nuclear ITS sequences. 1. Intergeneric relationships and polyphyly of Orchis sensu lato. Lindleyana 12: 89–109.
  • Rieseberg, L.H. (1997) Hybrid origins of plant species. Annual Review of Ecology, Evolution, and Systematics 28: 359–389.
  • Rieseberg, L.H., Whitton, J. & Linder, C.R. (1996) Molecular marker incongruence in plant hybrid zones and phylogenetic trees. Acta Botanica Neerlandica 45: 243–262.
  • Shipunov, A.B., Fay, M.F., Pillon, Y., Bateman, R.M. & Chase, M.W. (2004) Dactylorhiza (Orchidaceae) in European Russia: Combined molecular and morphological analysis. American Journal of Botany 91: 1419–1426.
  • Small, R.L., Ryburn, J.A., Cronn, R.C., Seelanan, T. & Wendel, J.F. (1998) The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301–1315.
  • Sramkó, G. (2008) Sequence variability of the nrITS in the Ophrys fuciflora species-complex of the Mediterranean bee-orchid (Ophrys L.) genus. Department of Botany. University of Debrecen, Debrecen.
  • Sramko, G., Attila, M.V., Hawkins, J.A. & Bateman, R.M .(2014) Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). Annals of Botany 114: 1609–1626. doi: 10.1093/aob/mcu179
  • Sramkó, G., Gulyás, G., Matus, G., Rudnóy, S., Illyés, Z., Bratek, Z. & Molnár, A. (2008) Leaf width, nrDNA and cpDNA its sequence variation within central European Bulbocodium vernum and B. versicolor (Colchicaceae) populations: Are there really two taxa? Acta Biologica Academiae Scientiarum Hungaricae 59: 103–114.
  • Sramkó, G., Molnár, V.A., Hawkins, J.A. & Bateman, R.M. (2011) Evolution of the Eurasiatic genus Himantoglossum(Orchideae, Orchidoideae): an integrativephylogenetic approach. In: In: Abstracts of the XVIII International Botanical Congress. Comittee of the XVIII IBC 2011, Melbourne, pp. 286–287.
  • Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
  • White, T.J., Bruns, T.D., Lee, S. & Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (Eds.) PCR protocols: A guide to methods and applications. Academic Press, San-Diego, pp. 315–322.
  • Won, H. & Renner, S.S. (2005) The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Molecular Phylogenetics and Evolution 36: 581–597. doi: 10.1016/j.ympev.2005.03.011
  • Zimmer, E.A. & Wen, J. (2012) Using nuclear gene data for plant phylogenetics: Progress and prospects. Molecular Phylogenetics and Evolution 65: 774–785. doi: 10.1016/j.ympev.2012.07.015
There are 29 citations in total.

Details

Primary Language English
Journal Section Makaleler
Authors

Kaan Hürkan 0000-0001-5330-7442

Kemal Melih Taşkın This is me 0000-0002-3746-0508

Project Number BAP FBA-2015-415
Publication Date March 4, 2021
Submission Date September 5, 2019
Acceptance Date October 29, 2019
Published in Issue Year 2021 Volume: 27 Issue: 1

Cite

APA Hürkan, K., & Taşkın, K. M. (2021). Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae). Journal of Agricultural Sciences, 27(1), 69-75. https://doi.org/10.15832/ankutbd.615848

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