Plant Systematics and Evolution

, Volume 277, Issue 1–2, pp 75–84

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

  • Kurt M. Neubig
  • W. Mark Whitten
  • Barbara S. Carlsward
  • Mario A. Blanco
  • Lorena Endara
  • Norris H. Williams
  • Michael Moore
Original Article


Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield phylogenetic structure at various levels of a tree (i.e., along the spine and at the tips of the branches). Here, we demonstrate the phylogenetic utility of a heretofore unused portion of a plastid protein-coding gene, hypothetical chloroplast open reading frame 1 (ycf1), in orchids. All portions of ycf1 examined are highly variable, yet alignable across Orchidaceae, and are phylogenetically informative at the level of species. In Orchidaceae, ycf1 is more variable than matK both in total number of parsimony informative characters and in percent variability. The nrITS region is more variable than ycf1, but is more difficult to align. Although we only demonstrate the phylogenetic utility of ycf1 in orchids, it is likely to be similarly useful among other plant taxa.


Chloroplast nrITS matOrchidaceae Phylogeny Molecular systematics ycf


  1. Asano T, Tsudzuki T, Takahashi S, Shimada H, Kadowaki K (2004) Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Research 11:93–99PubMedCrossRefGoogle Scholar
  2. Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard 82:247–277CrossRefGoogle Scholar
  3. Buckley TR, Simon C, Shimodaira H, Chambers GK (2001) Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology. Molec Biol Evol 18:223–234PubMedGoogle Scholar
  4. Cameron K (2002) Molecular systematics of Orchidaceae: a literature review and an example using five plastid genes. In: Nair H (ed) Proceedings of the 17th World Orchid Conference. Shah Alam, MalaysiaGoogle Scholar
  5. Cameron KM (2004) Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae. Molec Phylogenet Evol 31:1157–1180PubMedCrossRefGoogle Scholar
  6. Carlsward BS, Whitten WM, Williams NH, Bytebier B (2006) Molecular phylogenetics of Vandeae (Orchidaceae) and the evolution of leaflessness. Amer J Bot 93:770–786CrossRefGoogle Scholar
  7. Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chang CC, Chaw SM (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Molec Biol Evol 23:279–291PubMedCrossRefGoogle Scholar
  8. Chase MW, Freudenstein JV, Cameron KM, Barrett RL (2003) DNA data and Orchidaceae systematics: a new phylogenetic classification. In: Dixon KW, Kell SP, Barrett RL, Cribb PJ (eds) Orchid conservation. Natural History Publications, Kota Kinabalu, pp 69–89Google Scholar
  9. Cox AV (1997) PaupGap version 1.0: program and documentation. Royal Botanical Gardens, KewGoogle Scholar
  10. Drescher A, Ruf S, Calsa T Jr, Carrer H, Bock R (2000) The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Pl J 22:97–104CrossRefGoogle Scholar
  11. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  12. Freudenstein JV, van den Berg C, Goldman DH, Kores PJ, Molvray M, Chase MW (2004) An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. Amer J Bot 91:149–157CrossRefGoogle Scholar
  13. Jian S, Soltis PS, Gitzendanner MA, Moore MJ, Li R, Hendry TA, Qiu Y-L, Dhingra A, Bell CD, Soltis DE (2008) Resolving an ancient, rapid radiation in Saxifragales. Syst Biol 57:38–57PubMedCrossRefGoogle Scholar
  14. Johnson LA, Soltis DE (1998) Assessing congruence: empirical examples from molecular data. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer, Boston, pp 297–348Google Scholar
  15. Kim KJ, Lee HL (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research 11:247–261PubMedCrossRefGoogle Scholar
  16. Kocyan A, de Vogel EF, Gravendeel B (2008) Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step forward in understanding the evolution of the Aeridinae. Molec Phylogenet Evol 48:422–443CrossRefGoogle Scholar
  17. Maddison DR, Maddison WP (2000) MacClade 4: analysis of phylogeny and character evolution. Version 4.06. Sinauer Associates, SunderlandGoogle Scholar
  18. Milligan BG, Hampton JN, Palmer JD (1989) Dispersed repeats and structural reorganization in subclover chloroplast DNA. Molec Biol Evol 6:355–368PubMedGoogle Scholar
  19. Muller KF, Borsch T, Hilu KW (2006) Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F, and rbcL in basal angiosperms. Molec Phylogenet Evol 41:99–117PubMedCrossRefGoogle Scholar
  20. Ogihara Y, Terachi T, Sasakuma T (1988) Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci USA 85:8573–8577PubMedCrossRefGoogle Scholar
  21. Rambaut A (1996) Se-Al: sequence alignment editor, v2.0a11. University of Oxford, OxfordGoogle Scholar
  22. Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants. In: Henry RJ (ed) Plant diversity and evolution: genotypic and phenotypic variation in higher plants. CABI Publishing, Cambridge, pp 45–68Google Scholar
  23. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Amer J Bot 92:142–166CrossRefGoogle Scholar
  24. Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Amer J Bot 94:275–288CrossRefGoogle Scholar
  25. Shimada H, Sugiura M (1989) Pseudogenes and short repeated sequences in the rice chloroplast genome. Curr Genet 16:293–301PubMedCrossRefGoogle Scholar
  26. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369–381PubMedCrossRefGoogle Scholar
  27. Soltis DE, Soltis PS (1998) Choosing an approach and an appropriate gene for phylogenetic analysis. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer, Boston, pp 1–42Google Scholar
  28. Swofford DL (1999) PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer Associates, SunderlandGoogle Scholar
  29. Timme RE, Kuehl JV, Boore JL, Jansen RK (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Amer J Bot 94:302–312CrossRefGoogle Scholar
  30. van den Berg C, Goldman DH, Freudenstein JV, Pridgeon AM, Cameron KM, Chase M (2005) An overview of the phylogenetic relationships within Epidendroideae inferred from multiple DNA regions and recircumscription of Epidendreae and Arethuseae (Orchidaceae). Amer J Bot 92:613–624CrossRefGoogle Scholar
  31. Whitten MW, Williams NH, Chase MW (2000) Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: combined molecular evidence. Amer J Bot 87:1842–1856CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Kurt M. Neubig
    • 1
    • 2
  • W. Mark Whitten
    • 2
  • Barbara S. Carlsward
    • 3
  • Mario A. Blanco
    • 1
    • 4
  • Lorena Endara
    • 1
    • 2
  • Norris H. Williams
    • 2
  • Michael Moore
    • 5
  1. 1.Department of BotanyUniversity of FloridaGainesvilleUSA
  2. 2.Florida Museum of Natural HistoryUniversity of FloridaGainesvilleUSA
  3. 3.Department of Biological SciencesEastern Illinois UniversityCharlestonUSA
  4. 4.Jardín Botánico LankesterUniversidad de Costa RicaCartagoCosta Rica
  5. 5.Biology DepartmentOberlin College, Science Center K111OberlinUSA

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