참고문헌
- Bold, H.C., Alexopoulos, C.J., and Delevoryas, T. (1987). Morphology of Plants and Fungi, 4th ed. (New York: Harper and Row).
- Chumley, T.W., Palmer, J.D., Mower, J.P., Fourcade, H.M., Calie, P.J., Boore, J.L., and Jansen, R.K. (2006). The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol. Biol. Evol. 23, 2175-2190. https://doi.org/10.1093/molbev/msl089
- Cross, G.L. (1931a). Embryology of Osmunda cinnamomea. Bot. Gaz. 92, 210-217. https://doi.org/10.1086/334191
- Cross, G.L. (1931b). Meristem in Osmunda cinnamomea. Bot. Gaz. 91, 65-76. https://doi.org/10.1086/334126
- Downie, S.R., Llanas, E., and Katz-Downie, D.S. (1996). Multiple independent losses of the rpoC1 intron in angiosperm chloroplast DNA's. Syst. Bot. 21. 135-151. https://doi.org/10.2307/2419744
- Doyle, J.J., and Dolye, J.L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15.
- Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. https://doi.org/10.1093/nar/gkh340
- Freeberg, J.A., and Gifford Jr, E.M. (1984). The root apical meristem of Osmunda regalis. Am. J. Bot. 71, 558-563. https://doi.org/10.2307/2443331
- Gao, L., Yi, X., Yang, Y.X., Su, Y.J., and Wang, T. (2009). Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol. Biol. 9, 130. doi:10.1186/1471-2148-9-130
- Gao, L., Wang, B., Wang, Z.W., Zhou, Y., Su, Y.J., and Wang, T. (2013). Plastome sequences of Lygodium japonicum and Marsilea crenata reveal the genome organization transformation from basal ferns to core leptosporangiates. Genome Biol. Evol. 5, 1403-1407. https://doi.org/10.1093/gbe/evt099
- Gifford Jr, E. (1983). Concept of apical cells in bryophytes and pteridophytes. Annu. Rev. Plant Physiol. 34, 419-440. https://doi.org/10.1146/annurev.pp.34.060183.002223
- Good, C.W., and Taylor, T.N. (1975). The morphology and systematic position of calamitean elater?bearing spores. Geosci. Man 11, 133-139. https://doi.org/10.1080/00721395.1975.9989762
- Grewe, F., Guo, W., Gubbels, E.A., Hansen, A.K., and Mower, J.P. (2013). Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes. BMC Evol. Biol. 13, 8. https://doi.org/10.1186/1471-2148-13-8
- Guisinger, M.M., Kuehl, J.V., Boore, J.L., and Jansen, R.K. (2011). Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol. Biol. Evol. 28, 583-600. https://doi.org/10.1093/molbev/msq229
- Hasebe, M., and Iwatsuki, K. (1990). Chloroplast DNA from Adiantum capillus-veneris L., a fern species (Adiantaceae); clone bank, physical map and unusual gene localization in comparison with angiosperm chloroplast DNA. Curr. Genet. 17, 359-364. https://doi.org/10.1007/BF00314885
- Hiratsuka, J., Shimada, H., Whittier, R., Ishibashi, T., Sakamoto, M., Mori, M., Kondo, C., Honji, Y., Sun, C.R., Meng, B.Y., et al. (1989). The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217, 185-194. https://doi.org/10.1007/BF02464880
- Iwatsuki, K., Yamazaki, T., Boufford, D., and Ohba, H. (1995). Flora of Japan. Vol. I, Pteridophyta and Gymnospermae (Tokyo: Kodansha).
- Jansen, R.K., Raubeson, L.A., Boore, J.L., dePamphilis, C.W., Chumley, T.W., Haberle, R.C., Wyman, S.K., Alverson, A.J., Peery, R., Herman, S.J., et al. (2005). Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol. 395, 348-384. https://doi.org/10.1016/S0076-6879(05)95020-9
- Jansen, R.K., Cai, Z., Raubeson, L.A., Daniell, H., Depamphilis, C.W., Leebens-Mack, J., Muller, K.F., Guisinger-Bellian, M., Haberle, R.C., Hansen, A.K., et al. (2007). Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Natl. Acad. Sci. USA 104, 19369-19374. https://doi.org/10.1073/pnas.0709121104
- Karol, K.G., Arumuganathan, K., Boore, J.L., Duffy, A.M., Everett, K.D., Hall, J.D., Hansen, S.K., Kuehl, J.V., Mandoli, D.F., Mishler, B.D., et al. (2010). Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evol. Biol. 10, 321. https://doi.org/10.1186/1471-2148-10-321
- Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., et al. (2012). Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649. https://doi.org/10.1093/bioinformatics/bts199
- Kim, K.J., and Lee, H.L. (2004). Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11, 247-261. https://doi.org/10.1093/dnares/11.4.247
- Kim, Y.K., Park, C.W., and Kim, K.J. (2009). Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications. Mol. Cells 27, 365-381. https://doi.org/10.1007/s10059-009-0047-6
- Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., and Giegerich, R. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29, 4633-4642. https://doi.org/10.1093/nar/29.22.4633
- Lowe, T.M., and Eddy, S.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964. https://doi.org/10.1093/nar/25.5.0955
- Metzgar, J.S., Skog, J.E., Zimmer, E.A., and Pryer, K.M. (2008). The paraphyly of Osmunda is confirmed by phylogenetic analyses of seven plastid loci. Syst. Bot. 33, 31-36. https://doi.org/10.1600/036364408783887528
- Miller, M.A., Pfeiffer, W., and Schwartz, T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees; in Gateway Computing Environments Workshop (GCE), 2010 (IEEE).
- Moore, G.P. (1983). Slipped-mispairing and the evolution of introns. Trends Biochem. Sci. 8, 411-414. https://doi.org/10.1016/0968-0004(83)90307-9
- Palmer, J.D. (1986). Isolation and structural analysis of chloroplast DNA. Methods Enzymol. 118, 167-186. https://doi.org/10.1016/0076-6879(86)18072-4
- Palmer, J.D., and Stein, D.B. (1982). Chloroplast DNA from the fern Osmunda cinnamomea: physical organization, gene localization and comparison to angiosperm. Curr. Genet. 5, 165-170. https://doi.org/10.1007/BF00391801
- Palmer, J.D., and Stein, D.B. (1986). Conservation of chloroplast genome structure among vascular plants. Curr. Genet. 10, 823-833. https://doi.org/10.1007/BF00418529
- Posada, D., and Crandall, K.A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818. https://doi.org/10.1093/bioinformatics/14.9.817
- Pryer, K.M., Schneider, H., Smith, A.R., Cranfill, R., Wolf, P.G., Hunt, J.S., and Sipes, S.D. (2001). Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409, 618-622. https://doi.org/10.1038/35054555
- Pryer, K.M., Schuettpelz, E., Wolf, P.G., Schneider, H., Smith, A.R., and Cranfill, R. (2004). Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. Am. J. Bot. 91, 1582-1598. https://doi.org/10.3732/ajb.91.10.1582
- Pryer, K.M., Smith, A.R., and Rothfels, C. (2009). Polypodiopsida Cronquist, Takht. & Zimmerm. 1966. Ferns. Version 14, January 2009 (under construction). http://tolweb.org/Polypodiopsida/20615/2009.01.14 in The Tree of Life Web Project, http://tolweb.org/.
- Raubeson, L.A., and Jansen, R.K. (1992). Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255, 1697-1699. https://doi.org/10.1126/science.255.5052.1697
- Sablok, G., Nayak, K.C., Vazquez, F., and Tatarinova, T.V. (2011). Synonymous codon usage, GC(3), and evolutionary patterns across plastomes of three pooid model species: emerging grass genome models for monocots. Mol. Biotechnol. 49, 116-128. https://doi.org/10.1007/s12033-011-9383-9
- Schneider, H., Schuettpelz, E., Pryer, K.M., Cranfill, R., Magallon, S., and Lupia, R. (2004). Ferns diversified in the shadow of angiosperms. Nature 428, 553-557. https://doi.org/10.1038/nature02361
- Schuettpelz, E., and Pryer, K.M. (2007). Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes. Taxon 56, 1037-1050. https://doi.org/10.2307/25065903
- Schweitzer, H.-J. (1972). Die Mitteldevon-Flora von Lindlar (Rheinland). 3. Filicinae-Hyenia elegans Krausel & Weyland. Palaeontographica Abteilung B, 154-175.
- Smith, D.R. (2009). Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol. Biol. 71, 627-639. https://doi.org/10.1007/s11103-009-9545-3
- Smith, A.R., Pryer, K.M., Schuettpelz, E., Korall, P., Schneider, H., and Wolf, P.G. (2006). A classification for extant ferns. Taxon 55, 705-731. https://doi.org/10.2307/25065646
- Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. https://doi.org/10.1093/bioinformatics/btl446
- Stamatakis, A., Hoover, P., and Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57, 758-771. https://doi.org/10.1080/10635150802429642
- Swofford, D.L. (2003). PAUP; Phylogenetic Analysis Using Parsimony, version 4.0 b10 (Sunderland, Massachusetts: Sinauer Associates).
- Tangphatsornruang, S., Sangsrakru, D., Chanprasert, J., Uthaipaisanwong, P., Yoocha, T., Jomchai, N., and Tragoonrung, S. (2010). The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res. 17, 11-22. https://doi.org/10.1093/dnares/dsp025
- Taylor, E.L., Taylor, T.N., and Krings, M. (2009). Paleobotany: The Biology and Evolution of Fossil Plants (Burlington, Massachusetts: Elservier Ltd.).
- Thiede, J., Schmidt, S.A., and Rudolph, B. (2007) Phylogenetic implication of the chloroplast rpoC1 intron loss in the Aizoaceae (Caryophyllales). Biochem. Syst. Ecol. 35, 372-380. https://doi.org/10.1016/j.bse.2006.12.010
- Tidwell, W.D., and Ash, S.R. (1994). A review of selected Triassic to Early Cretaceous ferns. J. Plant Res. 107, 417-442. https://doi.org/10.1007/BF02344066
- Tryon, A., and Lugardon, B. (1991). Spores of the Pteridophyta. (New York: Springer-Verlag).
- Vetrivel, U., Arunkumar, V., and Dorairaj, S. (2007). ACUA: a software tool for automated codon usage analysis. Bioinformation 2, 62-63. https://doi.org/10.6026/97320630002062
- Wallace, R.S., and Cota, J.H. (1996). An intron loss in the chloroplast gene rpoC1 supports a monophyletic origin for the subfamily Cactoideae of the Cactaceae. Curr. Genet. 29, 275-281. https://doi.org/10.1007/BF02221558
- Wolf, P.G., Pryer, K.M., Ueda, K., Ito, M., Sano, R., Gastony, G., Yokoyama, J., Manhart, J., Murakami, N., and Crane, E. (1995). Fern phylogeny based on rbcL nucleotide sequences. Am. Fern J. 85, 134-181. https://doi.org/10.2307/1547807
- Wolf, P.G., Rowe, C.A., Sinclair, R.B., and Hasebe, M. (2003). Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res. 10, 59-65. https://doi.org/10.1093/dnares/10.2.59
- Wolf, P.G., Rowe, C.A., and Hasebe, M. (2004). High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene 339, 89-97. https://doi.org/10.1016/j.gene.2004.06.018
- Wolf, P.G., Roper, J.M., and Duffy, A.M. (2010). The evolution of chloroplast genome structure in ferns. Genome 53, 731-738. https://doi.org/10.1139/G10-061
- Wolf, P.G., Der, J.P., Duffy, A.M., Davidson, J.B., Grusz, A.L., and Pryer, K.M. (2011). The evolution of chloroplast genes and genomes in ferns. Plant Mol. Biol. 76, 251-261. https://doi.org/10.1007/s11103-010-9706-4
- Wright, F. (1990). The ‘effective number of codons' used in a gene. Gene 87, 23-29. https://doi.org/10.1016/0378-1119(90)90491-9
- Wu, C.S., Wang, Y.N., Liu, S.M., and Chaw, S.M. (2007). Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp proteincoding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol. Biol. Evol. 24, 1366-1379. https://doi.org/10.1093/molbev/msm059
- Wyman, S.K., Jansen, R.K., and Boore, J.L. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252-3255. https://doi.org/10.1093/bioinformatics/bth352
- Yatabe, Y., Nishida, H., and Murakami, N. (1999). Phylogeny of Osmundaceae inferred from rbcL nucleotide sequences and comparison to the fossil evidences. J. Plant Res. 112, 397-404. https://doi.org/10.1007/PL00013894
- Yi, D.K., and Kim, K.J. (2012). Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS One 7, e35872. https://doi.org/10.1371/journal.pone.0035872
- Yi, D.K., Lee, H.L., Sun, B.Y., Chung, M.Y., and Kim, K.J. (2012). The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids. Mol. Cells 33, 497-508. https://doi.org/10.1007/s10059-012-2281-6
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