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Plant Systematics and Evolution

, Volume 301, Issue 5, pp 1441–1453 | Cite as

ITS rDNA sequence comparisons resolve phylogenetic relationships in Orostachys subsection Appendiculatae (Crassulaceae)

  • Arthur Yu. Nikulin
  • Vyacheslav Yu. Nikulin
  • Svetlana B. Gonctharova
  • Andrey A. GontcharovEmail author
Original Article

Abstract

Orostachys (Crassulaceae) is a small genus of succulent plants having a predominantly East Asian distribution. Recent DNA sequence comparisons revealed polyphyletic nature of the genus and found distant relationship between its infrageneric taxa. Here we present the first molecular phylogeny of Orostachys subsection Appendiculatae based on a large number of ITS rDNA sequences representing most currently recognized members of the subsection and utilizing secondary structure information. Ribosomal spacer was a highly informative marker and provided a phylogenetic signal sufficient to resolve relationships at different scales, from affinities between species to a fine geographic structure in broadly sampled species. It was also conservative enough to allow unambiguous alignment and construction of consensus secondary structure models for ITS1 and ITS2. These models displayed a number of molecular synapomorphies defining most lineages established in our analyses. We revealed a major split in the subsection placing three species, O. spinosa, O. japonica and O. chanetii, into a strongly supported clade to the exclusion of O. thyrsiflora. Phenotypically distinct monotypic genus Meterostachys was also resolved as a part of the subsection’s clade and showed affinity to O. thyrsiflora. Our data suggested that morphology-based species concept for O. thyrsiflora requires reassessment.

Keywords

Crassulaceae Orostachys subsection Appendiculatae Meterostachys ITS rDNA Secondary structure Phylogeny 

Notes

Acknowledgments

We thank Shamil Abdullin, Viktor Bogatov, Roman Dudkin, Konstantin Kiselev, Yuri Ovchinnikov and Valentin Yakubov for sampling natural populations of O. spinosa; Marko Doboš for sharing his persona Orostachys collection and Sun Yan for assistance in sampling in Northern China. This study was supported by a RFBR grant (12-04-01379-a).

References

  1. Bailey CD, Carr TG, Harris SA, Hughes CE (2003) Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molec Phylogenet Evol 29(3):435–455CrossRefPubMedGoogle Scholar
  2. Bezdeleva TA (1995) Crassulaceae. In: Kharkevicz SS (ed) Plantae vasculares Orientis Extremi Sovietici, vol 7. Nauka, Sankt Petersburg, pp 214–235Google Scholar
  3. Bonfield JK, Smith KF, Staden R (1995) A new DNA sequence assembly program. Nucl Acids Res 23:4992–4999CrossRefGoogle Scholar
  4. Borissova AG (1939) Crassulaceae. In: Komarov VL (ed) Flora of USSR. Academiae Scientiarum URSS, Leningrad 9:8–134, 471–486Google Scholar
  5. Byalt VV (1997) Meterostachys sikokiana (Crassulaceae), a new species and genus in the flora of China. Bot Zhurn (Moscow & Leningrad) 82(7):128–130Google Scholar
  6. Byalt VV (1999) Monograph of the genus Orostachys Fisch. (Crassulaceae). Dissertation, Botanical Institute, Russian Academy of SciencesGoogle Scholar
  7. Byalt VV (2000) Conspectus generis Orostachys Fisch. (Crassulaceae). Novosti Sist Vyssh Rast 32:40–50Google Scholar
  8. Caisová L, Marin B, Sausen N, Pröschold T, Melkonian M (2011) Polyphyly of Chaetophora and Stigeolonium within the Chaetophorales (Chlorophyceae), revealed by sequence comparisons of nuclear-endoced SSU rRNA genes. J Phycol 47:164–177CrossRefGoogle Scholar
  9. Calonje M, Martin-Bravo S, Dobes C et al (2009) Non-coding nuclear DNA markers in phylogenetic reconstruction. Pl Syst Evol 282(3–4):257–280CrossRefGoogle Scholar
  10. Carrillo-Reyes P, Sosa V, Mort ME (2009) Molecular phylogeny of the Acre clade (Crassulaceae): dealing with the lack of definitions for Echeveria and Sedum. Molec Phylogenet Evol 53(1):267–276CrossRefPubMedGoogle Scholar
  11. Chen X, Liao B, Song J, Pang X, Han J, Chen S (2012) A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding. Gene 530(1):39–43CrossRefGoogle Scholar
  12. Darriba D, Taboada G, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Meth 9:772CrossRefGoogle Scholar
  13. Denduangboripant J, Cronk QC (2000) High intraindividual variation in internal transcribed spacer sequences in Aeschynanthus (Gesneriaceae): implications for phylogenetics. Proc R Soc Lond B 267(1451):1407–1415CrossRefGoogle Scholar
  14. Eggli U, ‘t Hart H, Nyffeler R (1995) Towards a consensus classification of the Crassulaceae. In: Eggli U (ed) Evolution and systematics of the Crassulaceae. Backhuys, Leiden, pp 173–192Google Scholar
  15. Elwood HJ, Olsen GJ, Sogin ML (1985) The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Molec Biol Evol 2:399–410PubMedGoogle Scholar
  16. Fairfield KN, Mort ME, Santos-Guerra A (2004) Phylogenetics and evolution of the Macaronesian members of the genus Aichryson (Crassulaceae) inferred from nuclear and chloroplast sequence data. Pl Syst Evol 248:71–83CrossRefGoogle Scholar
  17. Feliner GN, Rossello JA (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molec Phylogenet Evol 44(2):911–919CrossRefGoogle Scholar
  18. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  19. Fu KJ, Ohba H (2001) Crassulaceae. In: Wu ZY, Raven PH (eds) Flora of China. Science Press, Beijing, Missouri Botanical Garden Press, St. Louis, 8:202–268Google Scholar
  20. Galtier N, Gouy M, Gautier C (1996) Seaview and phylo-win: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548PubMedGoogle Scholar
  21. Gehrig H, Gaubmann O, Marx H, Schwarzrott D, Kluge M (2001) Molecular phylogeny of the genus Kalanchoe (Crassulaceae) inferred from nucleotide sequences of the ITS–1 and ITS–2 regions. Pl Sci 160:827–835CrossRefGoogle Scholar
  22. Gontcharova SB (2006) Sedoideae, Crassulaceae of the Russian Far East flora. Dalnauka, VladivostokGoogle Scholar
  23. Gontcharova SB, Gontcharov AA (2004) Sequence and secondary structure evolution of ITS rDNA in the family Crassulaceae. Chromosome Sci 8:142–144Google Scholar
  24. Gontcharova SB, Gontcharov AA (2009) Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC. Molec Biol 43:794–803CrossRefGoogle Scholar
  25. Gontcharova SB, Artyukova EV, Gontcharov AA (2006) Phylogenetic relationships among members of the subfamily Sedoideae (Crassulaceae) inferred from the ITS region sequences of nuclear rDNA. Russ J Genet 42:654–661CrossRefGoogle Scholar
  26. Gontcharova SB, Gontcharov AA, Stephenson R (2008) Analysis of phylogenetic relationships in the family Crassulaceae based on nucleotide sequences of ITS region of nuclear rDNA. Bot Zhurn (Moscow & Leningrad) 93:96–113Google Scholar
  27. Huelsenbeck JP, Ronoquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  28. Jorgensen TH, Frydenberg J (1999) Diversification in insular plants: inferring the phylogenetic relationship in Aeonium (Crassulaceae) using ITS sequences of nuclear ribosomal DNA. Nordic J Bot 19(5):613–621CrossRefGoogle Scholar
  29. Jorgensen TH, Olesen JM (2001) Adaptive radiation of island plants: evidence from Aeonium (Crassulaceae) of the Canary Islands. Bot J Linn Soc 132:223–240CrossRefGoogle Scholar
  30. Jung HJ, Choi J, Nam JH, Park HJ (2007) Anti-ulcerogenic effects of the flavonoid-rich fraction from the extract of Orostachys japonicus in mice. J Med Food 10(4):702–706CrossRefPubMedGoogle Scholar
  31. Kozyrenko MM, Gontcharova SB, Gontcharov AA (2013) Phylogenetic relationships among Orostachys subsection Orostachys species (Crassulaceae) based on nuclear and chloroplast DNA data. J Syst Evol 51(5):578–589CrossRefGoogle Scholar
  32. Krasnov EA, Saratikov AC, Surov YP (1979) Plants of the family Crassulaceae. Tomsk University, TomskGoogle Scholar
  33. Lee JH, Lee SJ, Park S et al (2011) Characterisation of flavonoids in Orostachys japonicus A. Berger using HPLC-MS/MS: contribution to the overall antioxidant effect. Food Chem 124:1627–1633CrossRefGoogle Scholar
  34. Lee GS, Lee HS, Kim SH et al (2014) Anti-cancer activity of the ethylacetate fraction from Orostachys japonicus for modulation of the signaling pathway in HepG2 human hepatoma cells. Food Sci Biotechnol 23(1):269–275CrossRefGoogle Scholar
  35. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefPubMedGoogle Scholar
  36. Marin B, Palm A, Klingberg M, Melkonian M (2003) Phylogeny and taxonomic revision of plastid-containing euglenophytes based on ssu rDNA sequence comparisons and synapomorphic signatures in the ssu rRNA secondary structure. Protist 154:99–145CrossRefPubMedGoogle Scholar
  37. Matyasek R, Renny-Byfield S, Fulnecek J et al (2012) Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genom 13:722CrossRefGoogle Scholar
  38. Mayuzumi S, Ohba H (2004) The phylogenetic position of East Asian Sedoideae (Crassulaceae) inferred from chloroplast and nuclear DNA sequences. Syst Bot 29:587–598CrossRefGoogle Scholar
  39. Mort ME, Soltis DE, Soltis PS, Francisco-Ortega J, Santos-Guerra A (2002) Phylogenetics and evolution of the Macaronesian clade of Crassulaceae inferred from nuclear and chloroplast sequence data. Syst Bot 27:271–288Google Scholar
  40. Mort ME, LevsenN Randle CP, Jaarsveld EV, Palmer A (2005) Phylogenetics and diversification of Cotyledon (Crassulaceae) inferred from nuclear and chloroplast DNA sequence data. Am J Bot 92(7):1170–1176CrossRefPubMedGoogle Scholar
  41. Ohba H (1978) Generic and infrageneric classification of the Old World Sedoideae (Crassulaceae). J Fac Sci U Tokyo III 12:139–198Google Scholar
  42. Ohba H (1990) Notes towards a monograph of the genus Orostachys (Crassulaceae) (1). J Jap Bot 65:193–203Google Scholar
  43. Ohba H (2001) Crassulaceae. In: Iwatsuki K, Boufford DE, Ohba H (eds) Flora of Japan, vol 2b. Kodasha, Tokyo, pp 10–31Google Scholar
  44. Ohba H (2005) Orostachys. In: Eggli U (ed) Illustrated handbook of succulent plants: Crassulaceae. Springer, Berlin, pp 135–142Google Scholar
  45. Ohwi J (1953) Crassulaceae. Flora of Japan. Shibundo, Tokyo, pp 585–592Google Scholar
  46. Peng YY, Baum BR, Ren CZ et al (2010) The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae). Hereditas 147(5):183–204CrossRefPubMedGoogle Scholar
  47. Poczai P, Hyvönen J (2010) Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Molec Biol Rep 37(4):1897–1912CrossRefGoogle Scholar
  48. Ryu DS, Baek GO, Kim EY, Kim KH, Lee DS (2010) Effects of polysaccharides derived from Orostachys japonicus on induction of cell cycle arrest and apoptotic cell death in human colon cancer cells. BMB Rep 43(11):750–755CrossRefPubMedGoogle Scholar
  49. Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M (2006) 4SALE—a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinform 7:498CrossRefGoogle Scholar
  50. Simon UK, Trajanoski S, Kroneis T, Sedlmayr P, Guelly C, Guttenberger H (2012) Accession-specific haplotypes of the internal transcribed spacer region in Arabidopsis thaliana-a means for barcoding populations. Molec Biol Evol 29(9):2231–2239CrossRefPubMedGoogle Scholar
  51. Song J, Shi L, Li D, Sun Y, Niu Y et al (2012) Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PLoS One 7(8):e43971. doi: 10.1371/journal.pone.0043971 CrossRefPubMedCentralPubMedGoogle Scholar
  52. Sung SH, Jung WJ, Kim YC (2002) A novel flavonol lyxoside of Orostachys japonicus herb. Nat Prod Lett 16(1):29–32CrossRefPubMedGoogle Scholar
  53. Swofford DL (2002) PAUP* Phylogenetic analysis using parsimony (and other methods). Beta version 10. Sinauer Associates, SunderlandGoogle Scholar
  54. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molec Biol Evol 28:2731–2739CrossRefPubMedCentralPubMedGoogle Scholar
  55. Telford MJ (2002) Cladistic analyses of molecular characters: the good, the bad and the ugly. Contr Zool 71(1–3):93–100Google Scholar
  56. Thiede J, Eggli U (2007) Crassulaceae DC. In: Kubitzki K (ed) The families and genera of vascular plants. Springer, Berlin, pp 83–118Google Scholar
  57. Vegetative resources of the USSR (1990) Flowering plants, their chemical composition, use. Families Caprifoliaceae–Plantaginaceae. Nauka, LeningradGoogle Scholar
  58. Wen J, Zimmer EA (1996) Phylogeny of Panax L. (the Ginseng Genus, Araliaceae): inference from ITS sequences of nuclear ribosomal DNA. Molec Phylogenet Evol 5:167–177CrossRefGoogle Scholar
  59. White TJ, Bruns T, Lee S, Taylor J (1990) Amplifcation and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322CrossRefGoogle Scholar
  60. Xiao LQ, Möller M, Zhu H (2010) High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: incomplete concerted evolution and the origin of pseudogenes. Molec Phylogenet Evol 55(1):168–177CrossRefPubMedGoogle Scholar
  61. Yoon NY, Min BS, Lee HK et al (2005) A potent anti-complementary acylated sterol glucoside from Orostachys japonicus. Arch Pharm Res 28(8):892–896CrossRefPubMedGoogle Scholar
  62. Yost JM, Bontrager M, McCabe SW et al (2013) Phylogenetic relationships and evolution in Dudleya (Crassulaceae). Syst Botany 38(4):1096–1104CrossRefGoogle Scholar
  63. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 31:3406–3415CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer-Verlag Wien 2014

Authors and Affiliations

  • Arthur Yu. Nikulin
    • 1
  • Vyacheslav Yu. Nikulin
    • 1
  • Svetlana B. Gonctharova
    • 2
  • Andrey A. Gontcharov
    • 1
    Email author
  1. 1.Institute of Biology and Soil Science FEB RASVladivostokRussia
  2. 2.Botanical garden-institute FEB RASVladivostokRussia

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