Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae)

American Journal of Botany

Volumn 95, Issue 4, 2008, Pages 498-505

  Freudenstein, John V ^a   Senyo, Diana M ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b KENT STATE UNIVERSITY   (United States)

Author keywords

Corallorhiza; matK; Molecular evolution; Orchidaceae; Plastid DNA

Indexed keywords

DNA; EVOLUTION; MONOCOTYLEDON; PHYLOGENY; PLASTID;

APLECTRUM; CORALLORHIZA; CORALLORHIZA BENTLEYI; CORALLORHIZA BULBOSA; CORALLORHIZA MACULATA; CREMASTRA; EPIDENDROIDEAE; GOVENIA; ORCHIDACEAE; WULLSCHLAEGELIA APHYLLA;

EID: 43049130772     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.95.4.498     Document Type: Article

References (52)

1. BARTHET, M. M., AND K. W. HILU. 2007. Expression of matK: Functional and evolutionary implications. American Journal of Botany 94: 1402-1412.
2. BOUFFORD, D. E., AND S. A. SPONGBERG. 1983. Eastern Asian-eastern North American phytogeographical relationships - a history from the time of Linnaeus to the twentieth century. Annals of the Missouri Botanical Garden 70: 423-439.
3. CAMERON, K. C., M. W. CHASE, W. R. ANDERSON, AND H. G. HILLS. 2001. Molecular systematics of Malpighiaceae: Evidence from plastid rbcL and matK sequences. American Journal of Botany 88: 1847-1862.
4. CHASE, M. W., K. M. CAMERON, R. L. BARRETT, AND J. V. FREUDENSTEIN. 2003. DNA data and Orchidaceae systematics: A new phylogenetic classification. In K. M. Dixon, S. P. Kell, R. L. Barrett, and P. J. Cribb [eds.], Orchid conservation, 69-89. Natural History Publications, Kota Kinabalu, Sabah, Malaysia.
5. CHEN, S.-C. 1983. A comparison of orchid floras of temperate North America and eastern Asia. Annals of the Missouri Botanical Garden 70: 713-723.
6. CHUANG, S.- L., AND J.-M. HU. 2004. The evolution of chloroplast matK genes, including identification of new homologues from Ophioglossum petiolatum and two lycophytes. Taiwania 49: 273-287.
7. DEPAMPHILIS, C. W., AND J. D. PALMER. 1990. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348: 337-339.
8. DOYLE, J. J., AND J. L. DOYLE. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
9. DRESSLER, R. L. 1993. Phylogeny and classification of the orchid family. Cambridge University Press, Cambridge, UK.
10. EMS, S. C., C. W. MORDEN, C. K. DIXON, K. H. WOLFE, C. W. DEPAMPHILIS, AND J. D. PALMER. 1995. Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Molecular Biology 29: 721-733.
11. FARRIS, J. S., V. A. ALBERT, M. KÄLLERSJÖ , D. L. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99-124.
12. FREUDENSTEIN, J. V. 1994a. Character transformation and relationships in Corallorhiza (Orchidaceae: Epidendroideae). II. Structural features and phylogenetic analysis. American Journal of Botany 81: 1458-1467.
13. FREUDENSTEIN, J. V. 1994b. Gynostemium structure and relationships of the Corallorhizinae (Orchidaceae: Epidendroideae). Plant Systematics and Evolution 193: 1-19.
14. FREUDENSTEIN, J. V. 1997. A monograph of Corallorhiza. Harvard Papers in Botany 10: 5-52.
15. FREUDENSTEIN, J. V. 1999a. A new species of Corallorhiza from West Virginia, USA. Novon 9: 511-513.
16. FREUDENSTEIN, J. V. 1999b. Relationships and character transformation in Pyroloideae (Ericaceae) based on ITS sequences, morphology, and development. Systematic Botany 24: 398-408.
17. FREUDENSTEIN, J. V., AND M. W. CHASE. 2001. Analysis of mitochondrial nad 1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters. Systematic Botany 26: 643-657.
18. FREUDENSTEIN, J. V., AND J. J. DOYLE. 1994. Character transformation and relationships in Corallorhiza (Orchidaceae: Epidendroideae). I. Plastid DNA. American Journal of Botany 81: 1449-1457.
19. GOLDMAN, D. H., J. V. FREUDENSTEIN, P. J. KORES, M. MOLVRAY, D. C. JARRELL, W. M. WHITTEN, K. M. CAMERON, AND M. W. CHASE. 2001. Phylogenetics of Arethuseae (Orchidaceae) based on plastid matK and rbcL sequences. Systematic Botany 26: 670-695.
20. GOLOBOFF, P. 1999. Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15: 415-428.
21. GOLOBOFF, P., J. FARRIS, AND K. NIXON. 2003. TNT: Tree analysis using new technology. Program and documentation available from the authors and at website http:// www.zmuc.dk/public/phylogeny/TNT/.
22. GOTT, J. M., AND R. B. EMESON. 2000. Functions and mechanisms of RNA editing. Annual Review of Genetics 34: 499-531.
23. GRAY, M. W. 2003. Diversity and evolution of mitochondrial RNA editing systems. International Union of Biochemistry and Molecular Biology Life 55: 227-233.
24. HAUSNER, G., R. OLSON, D. SIMON, I. JOHNSON, E. R. SANDERS, K. G. KAROL, R. M. MCCOURT, AND S. ZIMMERLY. 2006. Origin and evolution of the chloroplast trnK (matK ) intron: A model for evolution of group II intron RNA structures. Molecular Biology and Evolution 23: 380-391.
25. HESS, W. R., B. HOCH, P. ZELTZ, T. HÜBSCHMANN, H. KÖSSEL, AND T. BÖRNER. 1994. Inefficient rpl2 splicing inn barley mutants with ribosome-deficient plastids. Plant Cell 6: 1455-1465.
26. HILU, K. W., AND L. A. ALICE. 1999. Evolutionary implications of matK indels in Poaceae. American Journal of Botany 86: 1735-1741.
27. HILU, K. W., T. BORSCH, K. MÜLLER, D. E. SOLTIS, P. S. SOLTIS, V. SAVOLAINEN, M. W. CHASE, M. P. POWELL, L. A. ALICE, R. EVANS, H. SAUQUEST, C. NEINHUIS, T. A. B. SLOTTA, J. G. ROHWER, C. S. CAMPBELL, AND L. W. CHATROU. 2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: 1758-1776.
28. KORES, P. J., P. WESTON, M. MOLVRAY, AND M. W. CHASE. 2000. Phylogenetic relationships within Diurideae:Inferences from plastid matK DNA sequences. In K. L. Wilson and D. A. Morrison [eds.], Monocots: Systematics and evolution, 449-456. CSIRO Publishing, Collingwood, Victoria, Australia.
29. LI, W.- H. 1997. Molecular evolution. Sinauer, Sunderland, MA.
30. MAEKAWA, F. 1971. The wild orchids of Japan in colour. Seibundoshinkousha, Tokyo, Japan.
31. MICHEL, F., K. UMESONO, AND H. OZEKI. 1989. Comparative and functional anatomy of group II catalytic introns - a review. Gene 82: 5-30.
32. MOHR, G., P. S. PERLMAN, AND A. M. LAMBOWITZ. 1993. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Research 21: 4991-4997.
33. MOLVRAY, M., P. J. KORES, AND M. W. CHASE. 2000. Polyphyly of mycoheterotrophic orchids and functional influences on floral and molecular characters. In K. L. Wilson and D. A. Morrison [eds.], Monocots: Systematics and evolution, 441-448. CSIRO Publishing, Collingwood, Victoria, Australia.
34. RASMUSSEN, F. N. 1982. The gynostemium of the neottioid orchids. Opera Botanica 65: 1-96.
35. SIMMONS, M. P., AND H. OCHOTERENA. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
36. SOLTIS, D. E., AND P. S. SOLTIS. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II: DNA sequencing, 1-42. Kluwer, Boston, Massachusetts, USA.
37. STAMATAKIS, A. 2006. RaxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22: 2688-2690.
38. STEELE, K. P., AND R. VILGALYS. 1994. Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany 19: 126-142.
39. SWOFFORD, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b. Sinauer, Sunderland, MA, USA.
40. THOMPSON, J. D., T. J. GIBSON, F. PLEWNIAK, F. JEANMOUGIN, AND D. G. HIGGINS. 1997. The Clustal_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.
41. TILLICH, M., P. LEHWARK, B. R. MORTON, AND U. G. MAIER. 2006. The evolution of chloroplast DNA editing. Molecular Biology and Evolution 23: 1912-1921.
42. VOGEL, J., T. BÖRNER, AND W. R. HESS. 1999. Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants. Nucleic Acids Research 27: 3866-3874.
43. WEN, J. 1999. Evoluton of eastern Asian and eastern North American disjunction distributions in flowering plants. Annual Review of Ecology and Systematics 30: 421-455.
44. WHITTEN, W. M., N. H. WILLIAMS, AND M. W. CHASE. 2000. Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: Combined molecular evidence. American Journal of Botany 87: 1842-1856.
45. WOLF, P. G., C. A. ROWE, R. B. SINCLAIR, AND M. HASEBE. 2003. Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Research 10: 59-65.
46. WOLFE, A. D., AND C. W. DEPAMPHILIS. 1997. Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche. Plant Molecular Biology 33: 965-977.
47. WOLFE, K. H. 1991. Protein-coding genes in chloroplast DNA: Compilation of nucleotide sequences, data base entries, and rates of molecular evolution. In L. Bogorad and I. K. Vasil [eds.], The photosynthetic apparatus: Molecular biology and operation, vol. 7B, Cell culture and somatic cell genetics of plants, 467-482. Academic Press, San Diego, California, USA.
48. WOLFE, K. H., C. W. MORDEN, AND J. D. PALMER. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy of Sciences, USA 89: 10648-10652.
49. XIANG, Q.- Y., D. E. SOLTIS, AND P. S. SOLTIS. 1998a. Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences. American Journal of Botany 85: 285-297.
50. XIANG, Q.- Y., D. E. SOLTIS, AND P. S. SOLTIS. 1998b. The eastern Asian and eastern and wstern North American floristic disjunction: Congruent phylogenetic patterns in seven diverse genera. Molecular Phylogenetics and Evolution 10: 178-190.
51. YOUNG, N. D., AND C. W. DEPAMPHILIS. 2000. Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants. Molecular Biology and Evolution 17: 1933-1941.
52. YOUNG, N. D., K. E. STEINER, AND C. W. DEPAMPHILIS. 1999. The evolution of parasitism in Scrophulariaceae/Orobanchaceae: Plastid gene sequences refute an evolutionary transition series. Annals of the Missouri Botanical Garden 86: 876-893.