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Phylogeny and genetic variation in the genus Eranthis using nrITS and cpIS single nucleotide polymorphisms

Horticulture, Environment, and Biotechnology volume 60, pages 239–252 (2019)Cite this article

A Correction to this article was published on 08 May 2019

This article has been updated

Abstract

The relationships among species in the genus Eranthis Salisb. were investigated using single nucleotide polymorphisms (SNPs) of the nuclear DNA internal transcribed spacer 1, 2 region (nrITS) and the chloroplast trnL-trnF interspacer region (cpIS). Phylogenetic relationships based on the nrITS and cpIS were inferred with posterior probabilities with STRUCTURE analysis and the neighbor-joining method. Two major clades from nrITS and cpIS were consistent with species with yellow sepals in E. hyemalis, E. cilicica, E. longistipitata and the hybrid E. ×tubergenii; and white sepals in E. sibirica, E. longituba, E. albiflora, E. stellata, E. pungdoensis, E. byunsanensis, and E. pinnatifida. The phylogenetic tree of nrITS formed more subclades than the tree of cpIS, which suggested that nrITS SNPs are useful molecular markers for phylogenetic studies in the genus Eranthis. Only the SNPs of cpIS in E. pungdoensis accessions had a deletion at positions 259–420, and the posterior probability values (PPVs) assigned E. pungdoensis to population 4, which suggested that E. pungdoensis is different from E. byunsanensis. Therefore, E. byunsanensis and E. pungdoensis are considered to be true-to-type based on q-values because the PPVs were greater than 0.9 in both species based on the STRUCTURE analysis of nrITS SNPs. Significant genetic variation in E. stellata collected in Goesan-kun and Mt. Mugap, Korea indicated a potential gene flow among closely related E. byunsanensis, E. pinnatifida, E. sibirica, and E. stellata that could be due to geographic proximity in their distributions. E. stellata from Mt. Mugap showed mixed PPVs for E. stellata and E. byunsanensis, therefore, E. byunsanensis might be a possible hybrid origin for E. stellata collected from Goesan-kun and Mt. Mugap.

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Change history

  • 08 May 2019

    The original version of this article unfortunately contained a mistake. The name of Chin-Sung Chang was presented incorrectly. The corrected author list is given above.

References

  • Álevrez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434

    Article  CAS  Google Scholar 

  • Amundsen K, Warnke S (2011) Species relationships in the genus Agrostis based on flow cytometry and MITE-display molecular markers. Crop Sci 51:1224–1231

    Article  Google Scholar 

  • Baldwin BG (1992) Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. Mol Phylogenet Evol 1:1–16

    Article  Google Scholar 

  • Boens W (2014) The genus Eranthis, heralds of the end of winter. International Rock Gardener. ISSN 2053-7557, The Scottish Rock Garden Club, UK, pp 2–24

  • Bortiri E, Oh SH, Jiang J, Baggett S, Grander A, Weeks C, Buckingham M, Potter D, Parfitt DE (2001) Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA. Syst Bot 26:797–807

    Google Scholar 

  • Duminil J, De Michele M (2009) Plant species delimitation: a comparison of morphological and molecular markers. Plant Biosyst 143:528–542

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol 39:783–791

    Article  Google Scholar 

  • Gil HY, Lee EH, Choi IY, Roh MS, Chang CS (2011) A genetic study of Pinus parviflora on Ulleung Island of Korea, Compared to P. parviflora of Japan and P. armandii of China. Silvae Genet 60:233–240

    Article  Google Scholar 

  • Hoot SB, Renznicek AA, Palmer JD (1994) Phylogenetic relationships in Anemone (Ranunculaceae) based on morphology and chloroplast DNA. Syst Bot 19:169–200

    Article  Google Scholar 

  • Hubisz M, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332

    Article  PubMed  PubMed Central  Google Scholar 

  • Joung YH, Suh JK, Lee NS, Eum SM, Choj I-Y, Roh MS (2010) Identification of Hydrangeaceae ccessions of wild origin from Jeju, Korea, using molecular markers. Plant Genet Resour 8:235–241

    Article  CAS  Google Scholar 

  • Komarov VL (1970) Genus 513. Eranthis Salisb. Flora of the USSR (Translated from Russian, Izdatel’stvo Akademii Nauk SSSR Moskva-Leningrad 1937). Vol. 7. Ranales and Rhoeadales (Volume Ed. BK Shishkin), Israel Program for Scientific Translations, Jerusalem, Israel, pp 48–50

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee YN (2004) I. New taxa of Korean flora. Bull Korea Pl Res 4:2–4 (in Korean)

    Google Scholar 

  • Lee Y, Lee CS (2007) Eranthis byunsanensis B. Sun for. disepalis Y.Lee, for nov. Bull Korea Pl Res 7:13

  • Lee NS, Yeau SH, Park JO, Roh MS (2006) Molecular evidence for hybridization of Ilex × wandoensis (Aquifoliaceae) by RAPD analysis. J Plant Biol 49:491–497

    Article  CAS  Google Scholar 

  • Lee AK, Yuan T, Suh JK, Choi DS, Choi IK, Roh MS, Joung YH, Koh JY, Lee JS (2010) Pulsatilla tongkangensis, a new hybrid swarm population hybridized with P. koreana based on RAPD and SNPs of chloroplast DNA. Hortic Environ Biotechnol 51:409–421

    CAS  Google Scholar 

  • Lee AK, Hong J, Bauchan GR, Park SH, Joung JH (2012a) Confirmation of hybrid origin of Cyrtanthus based on the sequence analysis of internal transcribed spacer. Sci Hortic 144:150–153

    Article  CAS  Google Scholar 

  • Lee CS, Yeau SH, Lee NS (2012b) Taxonomic status and genetic variation of Korean endemic plants, Eranthis byunsanensis and Eranthis pungdoensis (Ranunculaceae) based on nrDNA ITS and cpDNA sequences. J Plant Biol 55:165–177

    Article  Google Scholar 

  • Lexer C, Joseph JA, Loo M, Barbará T, Heinze B, Bartha D, Castiglione S, Fay MF, Buerkle CA (2010) Genomic admixture analysis in European Populus spp. reveals unexpected patterns of reproductive isolation and mating. Genetics 186:699–712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L, Tamura M (2001) Etranthis Salisbury, Trans. Linn. Soc. London 8:303. 1807, nom. cons. Flora China 6:148–149

    Google Scholar 

  • Linnaeus C (1753) Species Plantarum. Holmiae (Stockholm), impensis. Laurentii Salvii, Sweden

  • Oh BU, Ji SJ (2009) Eranthis pungdoensis B.U. Oh: a new species of Eranthis (Ranunculaceae) from Korea. Korean J Plant Taxon 39:86–88

    Article  Google Scholar 

  • Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 29:4–98

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rauscher JT, Doyle JJ, Brown AHD (2002) Interna transcribed spacer repeat-specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex. Mol Ecol 11:2691–2702

    Article  CAS  PubMed  Google Scholar 

  • Rogers SO, Bendich AJ (1987) Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol 9:509–520

    Article  CAS  PubMed  Google Scholar 

  • Salisbury RA (1807) Observations on the Genera of Trollius, Eranthis, Helleborus, Coptis and Isopyrum. Trans R Soc Edinb 8:300–307

    Google Scholar 

  • Sun BY, Kim CH, Kim T J (1993) A new species of Eranthis (Ranunculaceae) from Korea: E. byunsanensis. Korean J Plant Taxon 23:21–26. (In Korean with English abstract)

  • Turrili WB (1922) Abnormal flowers in Eranthis. Ann Bot 36:131–133

    Article  Google Scholar 

  • Vähä JP, Primmer CR (2006) Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 15:63–72

    Article  CAS  PubMed  Google Scholar 

  • Wahlsteen E (2015) An Eranthis riddle. Alpine Gardener 83:102–107

    Google Scholar 

  • Wahlsteen E (2016) The genus Eranthis. http://the-genus-eranthis.blogspot.com. Accessed Oct 20 2016

  • Wang WT (1987) Notulae de Ranunculaceis sinensibus (XII). Bull Bot Res 7:95–114 (In Chinese with Latin)

    Google Scholar 

  • Wang WT (1997) Notulae de Ranunculaceis sinensibus (XXI) Guihaih 17(1):1-15. (In Chinese with English summary)

  • Wang WT, Hsiao PK (1965) Notulae de Ranunculaceis sinensibus II. Acta Phytot Sin 10:49-103 with VI plates. Additamentum I. Published Online: Dec. 1965. (In Chinese with Latin)

  • Yuan T, Wang LY, Roh MS (2010) Confirmation of Clematis hybrids using molecular markers. Scientia Hortic 125:136–145

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This project was co-funded in part by the “Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01389401)” Rural Development Administration, Republic of Korea awarded to YH Joung and the Swedish Garden Societies (Skånska trädgårdsföreningen, STA Skånekretsen, STA Hallandskretsen, and Trädgårdsamatörerna Göteborg. We thank Dr. Mark S. Roh who had conceived the project, made arrangements for germplasm collection, and worked with all contributors who had in-depth knowledge of all aspects of fieldwork and accession identification. Dr. Roh assisted all authors to prepare the manuscript prior to submission. We thank those who contributed leaf samples for DNA analysis and imaging, and who gave permission to use their images: G.Moen, R. Drew, J. Jilak, B. Żuraw, S. Ritzenfeld, P. Woodward, S.S. Wu, Z-Yu Li, M. Koshioka, J. McKenney, S. Schwartzkopf, S. Pistorello, V. Scariot, V.Zilek, J. Ruksans, JS Chang, JK Lee, EJ Kim, KZ Riu, KH Chung, HJ Yang, NR Cho, and YH Kim. The image of E. pinnatifida was from the internet (http://carex.tumblr.com/post/74793560527/oakapples-winter-aconite-eranthis-hyemalis) and the image of E. stellata is from Is. Sahkalin (SA IS; http://www.wildbulbs.eu/eran.htm. Accessed May 17, 2017). The image of Eranthis ×tubergenii is copyrighted by Paige Woodward, Pacific Rim Native Plant Nursery.

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Author notes

  1. Seo Young Park and Mi Jin Jeon equally contributed to the project for carrying out experiment, analyses of data, and preparing the manuscript.

Authors and Affiliations

  1. Plant Molecular Biology Laboratory, School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea

    Seo Young Park, Mi Jin Jeon, Sang Hoon Ma & Young Hee Joung

  2. Department of Landscape Architecture, Planning and Management, Swedish University of Agricultural Sciences, Sundsvägen, 23053, Alnarp, Sweden

    Eric Wahlsteen

  3. Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA

    Keenan Amundsen

  4. Department of Environmental Horticulture, Dankook University, Cheonan, Chungcheongnam-do, 31116, Korea

    Ji Hee Kim & Jeung Keun Suh

  5. Agriculture and Life Sciences, Department of Forest Sciences, Seoul National University, Seoul, 08826, Korea

    Jin Sung Chang

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  1. Seo Young Park
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Correspondence to Young Hee Joung.

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Accession and collection information of the genus Eranthis (DOCX 18 kb)

13580_2018_113_MOESM2_ESM.tif

Sequencing chromatograms of nrITS PCR products of and E. hyemalis IT/LU 2 (A) and E. byunsanensis KR/NB 1 (B). The continuous double peaks shown in (A) and the heterozygous double peak was boxed in (B) (TIFF 806 kb)

Alignment of nrITS sequences among selected accessions (TIFF 18768 kb)

Alignment of cpIS sequences among selected accessions (TIFF 17551 kb)

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Park, S.Y., Jeon, M.J., Ma, S.H. et al. Phylogeny and genetic variation in the genus Eranthis using nrITS and cpIS single nucleotide polymorphisms. Hortic. Environ. Biotechnol. 60, 239–252 (2019). https://doi.org/10.1007/s13580-018-0113-0

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Keywords

  • Chloroplast trnL-trnF interspacer region
  • Floral morphology
  • Hybrid origin
  • Intraspecific variation
  • Nuclear ITS 1
  • 2 Region
  • STRUCTURE analysis