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DOI: http://dx.doi.org/10.11646/phytotaxa.402.2.3

DNA barcoding and phylogenetic relationships in Omphalogramma (Primulaceae) from the Hengduan Mountain region of China

YUAN HUANG, XIONG CHEN, JIAHUI CHEN, ZHIMIN LI

Abstract


One nuclear and three chloroplast DNA markers (internal transcribed spacer [ITS], rbcL, matK, and trnH-psbA) were evaluated from 39 accessions of Omphalogramma (Primulaceae) from the Hengduan Mountains, representing seven species. The discrimination power of the markers at the species level was 14.3% (rbcL), 28.4% (trnH-psbA), 42.9% (matK), and 100% (ITS). The mean value of genetic distance between species for ITS was more than 3-fold that of intraspecific distance; all species were distinguished. Species were differentiated by unique characters, and phylogenetic analysis showed that the Omphalogramma species formed two clear monophyletic clades comprising O. vincaeflora (bootstrapping: 96.8%) and remaining Omphalogramma species (bootstrapping: 97.5%). This study indicated that DNA barcoding is a useful technique in the phylogenetic and taxonomic description of Omphalogramma species.


Keywords


Eudicots, Omphalogramma, DNA barcoding, ITS, phylogenetic relationships

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References


Anderberg, A.A., Ståhl, B. & Källersjö, M. (1998) Phylogenetic relationships in the Primulales inferred from rbcL sequence data. Plant Systematics and Evolution 211: 93–102.

https://doi.org/10.1007/BF00984914

Balfour, B. (1920) Primula et Omphalogramma: Diagnoses Specierum Novarum. Notes from the Royal Botanical Garden, Edinburgh 13 (61): 1–24.

Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T. & Pang, X. (2010) Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLOS ONE 5 (1): e8613.

https://doi.org/10.1371/journal.pone.0008613

Conti, E., Suring, E., Boyd, D., Jorgensen, J., Grant, J. & Kelso, S. (2000) Phylogenetic relationships and character evolution in Primula L.: The usefulness of ITS sequence data. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology 134: 385–392.

https://doi.org/10.1080/11263500012331350535

de Vos, J.M., Hughes, C.E., Schneeweiss, G.M., Moore, B.R. & Conti, E. (2014) Heterostyly accelerates diversification via reduced extinction in primroses. Proceedings of the Royal Society B: Biological Sciences 281: 20140075.

https://doi.org/10.1098/rspb.2014.0075

Doyle, J.J. & Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.

Fletcher, H. (1949) The genus Omphalogramma. Notes from the Royal Botanic Garden, Edinburgh 20: 125–159.

Forrest, G. (1911) New or noteworthy plants. The Gardeners’ Chronicle: a weekly illustrated journal of horticulture and allied subjects, 3 ser 50: 242.

Franchet, A. (1887) Plantae Davidianae ex Sinarum Imperio. The Gardeners’ Chronicle: a weekly illustrated journal of horticulture and allied subjects, 3 ser 1: 574.

Franchet, A. (1898) Un nouveau genre de Primulacées de la tribu des Hottoniées. Bulletin de la Société botanique de France 45: 177–180.

https://doi.org/10.1080/00378941.1898.10830840

Handel-Mazzetti, H. (1922) Plantae novae Sinenses. Anzeiger der Akademie der Wissenschaften in Wien. Mathematische-naturwissenchaftliche Klasse 59: 248.

Hoang, D.T., Chernomor, O., Von Haeseler, A., Minh, B.Q. & Vinh, L.S. (2018) UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution 35: 518–522.

https://doi.org/10.1093/molbev/msx281

Hollingsworth, M.L., Clark, A., Forrest, L.L., Richardson, J.E., Pennington, R.T., Long, D.G., Cowan, R.S., Chase, M.W., Gaudeul, M. & Hollingsworth, P.M. (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Molecular Ecology Resources 9: 439–457.

https://doi.org/10.1111/j.1755-0998.2008.02439.x

Hollingsworth, P.M. (2011) Refining the DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 108: 19451–19452.

https://doi.org/10.1073/pnas.1116812108

Hu, Q. & Kelso, S. (1996) Primulaceae. In: Wu, C.Y. & Raven, P.H. (Eds.) Flora of China, Vol. 15. Science Press and Missouri Botanical Garden, Beijing and St Louis, pp. 185–188.

Huang, Y., Zhang, C., Blackmore, S., Li, D. & Wu, Z. (2006) A preliminary study on pollination biology of Omphalogramma souliei Franch.(Primulaceae), a species endemic to China. Plant Systematics and Evolution 261: 89–98.

https://doi.org/10.1007/s00606-006-0430-0

Huang, Y., Zhang, C. & Li, D. (2009) Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae): implications for its conservation. Journal of Systematics and Evolution 47: 103–109.

https://doi.org/10.1111/j.1759-6831.2009.00008.x

Kress, W.J. & Erickson, D.L. (2007) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLOS ONE 2 (6): e508.

https://doi.org/10.1371/journal.pone.0000508

Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A. & Janzen, D.H. (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102: 8369–8374.

https://doi.org/10.1073/pnas.0503123102

Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870–1874.

https://doi.org/10.1093/molbev/msw054

Léveillé, H. (1915) Catalogue des Plantes du Yun-Nan. Le Monde des Plantes 17: 2.

Li, D., Gao, L., Li, H., Wang, H., Ge, X., Liu, J., Chen, Z., Zhou, S., Chen, S. & Yang, J. (2011) Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences of the United States of America 108: 19641–19646.

https://doi.org/10.1073/pnas.1104551108

Linnaeus, C. (1753) Species Plantarum Ed. 1, Vol 1. Holmiae, 142 pp.

Liu, Z., Ci, X., Li, L., Li, H., Conran, J.G. & Li, J. (2017) DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. PLOS ONE 12 (4): e0175788.

https://doi.org/10.1371/journal.pone.0175788

Martins, L., Oberprieler, C. & Hellwig, F. (2003) A phylogenetic analysis of Primulaceae based on internal transcribed spacer (ITS) DNA sequence data. Plant Systematics and Evolution 237: 75–85.

https://doi.org/10.1007/s00606-002-0258-1

Mast, A.R., Kelso, S. & Conti, E. (2006) Are any primroses (Primula) primitively monomorphic? New Phytologist 171: 605–616.

https://doi.org/10.1111/j.1469-8137.2006.01700.x

Mast, A.R., Kelso, S., Richards, A.J., Lang, D.J., Feller, D.M. & Conti, E. (2001) Phylogenetic relationships in Primula L. and related genera (Primulaceae) based on noncoding chloroplast DNA. International Journal of Plant Sciences 162: 1381–1400.

https://doi.org/10.1086/323444

Meier, R., Shiyang, K., Vaidya, G. & Ng, P.K.L. (2006) DNA Barcoding and Taxonomy in Diptera: A Tale of High Intraspecific Variability and Low Identification Success. Systematic Biology 55: 715–728.

https://doi.org/10.1080/10635150600969864

Nguyen, L., Schmidt, H.A., Von Haeseler, A. & Minh, B.Q. (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Molecular Biology and Evolution 32: 268–274.

https://doi.org/10.1093/molbev/msu300

Pax, F. & Knuth, R. (1905) Primulaceae. In: Engler, A. (Ed.) Das Pflanzenreich, 22. Akademie der Wissenschaft, Berlin, pp. 1–107.

Primula Conference (1929) The Fourth Primula Conference 1928. Royal Horticultural Society, British, pp. 1–252.

Richards, J. (1993) Primula. 1st edn. Batsford, London, pp. 28–201.

Richards, J. (2003) Primula. 2st edn. Batsford, London, pp. 36–153.

Smith, W.W. & Forrest, G. (1923) New Primulaceae. Notes from the Royal Botanical Garden, Edinburgh 14 (68): 45–46.

Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876–4882.

https://doi.org/10.1093/nar/25.24.4876

Trifinopoulos, J., Nguyen, L., Von Haeseler, A. & Minh, B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44: 232–235.

https://doi.org/10.1093/nar/gkw256

Yan, H., Hao, G., Chiming, H.U. & Xuejun, G.E. (2011a) DNA barcoding in closely related species: A case study of Primula L. sect. Proliferae Pax (Primulaceae) in China. Journal of Systematics and Evolution 49: 225–236.

https://doi.org/10.1111/j.1759-6831.2011.00115.x

Yan, H., Hao, G., Hu, C. & Ge, X. (2011b) DNA barcoding in closely related species: A case study of Primula L. sect. Proliferae Pax (Primulaceae) in China. Journal of Systematics and Evolution 49: 225–236.

https://doi.org/10.1111/j.1759-6831.2011.00115.x

Yan, H., Liu, Y., Xie, X., Zhang, C., Hu, C., Hao, G. & Ge, X. (2015) DNA Barcoding Evaluation and Its Taxonomic Implications in the Species-Rich Genus Primula L. in China. PLOS one 10 (4): e0122903.

https://doi.org/10.1371/journal.pone.0122903

Yu, W., Huang, P., Ree, R.H., Liu, M., Li, D. & Wang, H. (2011) DNA barcoding of Pedicularis L. (Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus. Journal of Systematics and Evolution 49: 425–437.

https://doi.org/10.1111/j.1759-6831.2011.00154.x

Zhang, L. & Kadereit, J.W. (2002) The systematics of Soldanella (Primulaceae) based on morphological and molecular (ITS, AFLPs) evidence. Nordic Journal of Botany 22: 129–169.

https://doi.org/10.1111/j.1756-1051.2002.tb01360.x


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