TY - CHAP AU - Gifford, E. M. AU - Foster, A. S. PY - 1989 DA - 1989// BT - Morphology and evolution of vascular plants PB - W.H. Freeman and Company CY - New York ID - Gifford1989 ER - TY - CHAP AU - Chamberlain, C. J. PY - 1935 DA - 1935// BT - Gymnosperms: Structure and Function PB - University of Chicago Press CY - Chicago ID - Chamberlain1935 ER - TY - JOUR AU - Dilcher, D. L. AU - Bernardes-De-Oliveira, M. E. AU - Pons, D. AU - Lott, T. A. PY - 2005 DA - 2005// TI - Welwitschiaceae from the Lower Cretaceous of Northeastern Brazil JO - Am J Bot VL - 92 UR - https://doi.org/10.3732/ajb.92.8.1294 DO - 10.3732/ajb.92.8.1294 ID - Dilcher2005 ER - TY - JOUR AU - Magallon, S. AU - Sanderson, M. J. PY - 2002 DA - 2002// TI - Relationships among seed plants inferred from highly conserved genes: Sorting conflicting phylogenetic signals among ancient lineages JO - Am J Bot VL - 89 UR - https://doi.org/10.3732/ajb.89.12.1991 DO - 10.3732/ajb.89.12.1991 ID - Magallon2002 ER - TY - JOUR AU - Burleigh, J. G. AU - Mathews, S. PY - 2004 DA - 2004// TI - Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life JO - Am J Bot VL - 91 UR - https://doi.org/10.3732/ajb.91.10.1599 DO - 10.3732/ajb.91.10.1599 ID - Burleigh2004 ER - TY - JOUR AU - Doyle, J. A. AU - Donoghue, M. J. PY - 1986 DA - 1986// TI - Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach JO - Bot Rev VL - 52 UR - https://doi.org/10.1007/BF02861082 DO - 10.1007/BF02861082 ID - Doyle1986 ER - TY - JOUR AU - Rothwell, G. W. AU - Serbet, R. PY - 1994 DA - 1994// TI - Lignophyte phylogeny and the evolution of spermatophytes: a numerical cladistic analysis JO - Syst Bot VL - 19 UR - https://doi.org/10.2307/2419767 DO - 10.2307/2419767 ID - Rothwell1994 ER - TY - JOUR AU - Donoghue, M. J. AU - Doyle, J. A. PY - 2000 DA - 2000// TI - Seed plant phylogeny: Demise of the anthophyte hypothesis? JO - Curr Biol VL - 10 UR - https://doi.org/10.1016/S0960-9822(00)00304-3 DO - 10.1016/S0960-9822(00)00304-3 ID - Donoghue2000 ER - TY - JOUR AU - Rydin, C. AU - Kallersjo, M. AU - Friist, E. M. PY - 2002 DA - 2002// TI - Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: Conflicting data, rooting problems, and the monophyly of conifers JO - Int J Plant Sci VL - 163 UR - https://doi.org/10.1086/338321 DO - 10.1086/338321 ID - Rydin2002 ER - TY - JOUR AU - Soltis, D. E. AU - Soltis, P. S. AU - Zanis, M. J. PY - 2002 DA - 2002// TI - Phylogeny of seed plants based on evidence from eight genes JO - Am J Bot VL - 89 UR - https://doi.org/10.3732/ajb.89.10.1670 DO - 10.3732/ajb.89.10.1670 ID - Soltis2002 ER - TY - JOUR AU - Rai, H. S. AU - O'Brien, H. E. AU - Reeves, P. A. AU - Olmstead, R. G. AU - Graham, S. W. PY - 2003 DA - 2003// TI - Inference of higher-order relationships in the cycads from a large chloroplast data set JO - Mol Phylogenet Evol VL - 29 UR - https://doi.org/10.1016/S1055-7903(03)00131-3 DO - 10.1016/S1055-7903(03)00131-3 ID - Rai2003 ER - TY - JOUR AU - Chaw, S. M. AU - Zharkikh, A. AU - Sung, H. M. AU - Lau, T. C. AU - Li, W. H. PY - 1997 DA - 1997// TI - Molecular phylogeny of extant gymnosperms and seed plant evolution: Analysis of nuclear 18S rRNA sequences JO - Mol Biol Evol VL - 14 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025702 DO - 10.1093/oxfordjournals.molbev.a025702 ID - Chaw1997 ER - TY - JOUR AU - Qiu, Y. L. AU - Lee, J. H. AU - Bernasconi-Quadroni, F. AU - Soltis, D. E. AU - Soltis, P. S. AU - Zanis, M. AU - Zimmer, E. A. AU - Chen, Z. D. AU - Savolainen, V. AU - Chase, M. W. PY - 1999 DA - 1999// TI - The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes JO - Nature VL - 402 UR - https://doi.org/10.1038/46536 DO - 10.1038/46536 ID - Qiu1999 ER - TY - JOUR AU - Chaw, S. AU - Parkinson, C. L. AU - Cheng, Y. AU - Vincent, T. M. AU - Palmer, J. D. PY - 2000 DA - 2000// TI - Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.97.8.4086 DO - 10.1073/pnas.97.8.4086 ID - Chaw2000 ER - TY - JOUR AU - Bowe, L. M. AU - Coat, G. AU - dePamphilis, C. W. PY - 2000 DA - 2000// TI - Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.97.8.4092 DO - 10.1073/pnas.97.8.4092 ID - Bowe2000 ER - TY - JOUR AU - Felsenstein, J. PY - 1978 DA - 1978// TI - Cases in which parsimony or compatibility methods will be positively misleading JO - Syst Zool VL - 27 UR - https://doi.org/10.2307/2412923 DO - 10.2307/2412923 ID - Felsenstein1978 ER - TY - JOUR AU - Philippe, H. AU - Zhou, Y. AU - Brinkmann, H. AU - Rodrigue, N. AU - Delsuc, F. PY - 2005 DA - 2005// TI - Heterotachy and long-branch attraction in phylogenetics JO - BMC Evol Biol VL - 5 UR - https://doi.org/10.1186/1471-2148-5-50 DO - 10.1186/1471-2148-5-50 ID - Philippe2005 ER - TY - JOUR AU - Moreira, D. AU - Phillippe, H. PY - 2000 DA - 2000// TI - Molecular phylogeny: pitfalls and progress JO - Internatl Microbiol VL - 3 ID - Moreira2000 ER - TY - JOUR AU - Rokas, A. AU - Holland, P. W. H. PY - 2000 DA - 2000// TI - Rare genomic changes as a tool for phylogenetics JO - TREE VL - 15 ID - Rokas2000 ER - TY - JOUR AU - Boore, J. L. PY - 2006 DA - 2006// TI - The use of genome-level characters for phylogenetic reconstruction JO - TREE VL - 21 ID - Boore2006 ER - TY - JOUR AU - Wakasugi, T. AU - Tsudzuki, J. AU - Ito, S. AU - Nakashima, K. AU - Tsudzuki, T. AU - Sugiura, M. PY - 1994 DA - 1994// TI - Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii JO - Proc Natl Acad Sci USA VL - 91 UR - https://doi.org/10.1073/pnas.91.21.9794 DO - 10.1073/pnas.91.21.9794 ID - Wakasugi1994 ER - TY - JOUR AU - Wu, C. S. AU - Wang, Y. N. AU - Liu, S. M. AU - Chaw, S. M. PY - 2007 DA - 2007// TI - Chloroplast Genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm059 DO - 10.1093/molbev/msm059 ID - Wu2007 ER - TY - CHAP AU - Raubeson, L. A. AU - Jansen, R. K. ED - Henry, R. PY - 2005 DA - 2005// TI - Chloroplast genomes of plants BT - Diversity and Evolution of Plants – Genotypic and phenotypic variation in higher plants PB - CABI Publishing CY - London UR - https://doi.org/10.1079/9780851999043.0045 DO - 10.1079/9780851999043.0045 ID - Raubeson2005 ER - TY - JOUR AU - Shinozaki, K. AU - Ohme, M. AU - Tanaka, M. AU - Wakasugi, T. AU - Hayashida, N. AU - Matsubayashi, T. AU - Zaita, N. AU - Chunwongse, J. AU - Obokata, J. AU - Yamaguchishinozaki, K. AU - Ohto, C. AU - Torazawa, K. AU - Meng, B. Y. AU - Sugita, M. AU - Deno, H. AU - Kamogashira, T. AU - Yamada, K. AU - Kusuda, J. AU - Takaiwa, F. AU - Kato, A. AU - Tohdoh, N. AU - Shimada, H. AU - Sugiura, M. PY - 1986 DA - 1986// TI - The complete nucleotide sequence of the tobacco chloroplast genome – Its gene organization and expression JO - EMBO J VL - 5 ID - Shinozaki1986 ER - TY - CHAP AU - Downie, S. R. AU - Palmer, J. D. ED - Soltis, P. S. ED - Soltis, D. E. ED - Doyle, J. J. PY - 1992 DA - 1992// TI - Use of chloroplast DNA rearrangements in reconstructing plant phylogeny BT - Molecular Systematics of Plants PB - Chapman and Hall CY - New York UR - https://doi.org/10.1007/978-1-4615-3276-7_2 DO - 10.1007/978-1-4615-3276-7_2 ID - Downie1992 ER - TY - CHAP AU - Palmer, J. D. ED - Hermann, R. G. PY - 1991 DA - 1991// TI - Plastid chromosomes: structure and evolution BT - The molecular biology of plastids. Cell culture and somatic cell genetics of plants. 7A PB - Springer-Verlag CY - Vienna ID - Palmer1991 ER - TY - JOUR AU - Goremykin, V. V. AU - Hirsch-Ernst, K. I. AU - Wolfl, S. AU - Hellwig, F. H. PY - 2003 DA - 2003// TI - Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborellais not a basal angiosperm JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg159 DO - 10.1093/molbev/msg159 ID - Goremykin2003 ER - TY - JOUR AU - Raubeson, L. A. AU - Peery, R. AU - Chumley, T. W. AU - Dziubek, C. AU - Fourcade, H. M. AU - Boore, J. L. AU - Jansen, R. K. PY - 2007 DA - 2007// TI - Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macaranthus JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-174 DO - 10.1186/1471-2164-8-174 ID - Raubeson2007 ER - TY - JOUR AU - Cai, Z. Q. AU - Penaflor, C. AU - Kuehl, J. V. AU - Leebens-Mack, J. AU - Carlson, J. E. AU - dePamphilis, C. W. AU - Boore, J. L. AU - Jansen, R. K. PY - 2006 DA - 2006// TI - Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids JO - BMC Evol Biol VL - 6 UR - https://doi.org/10.1186/1471-2148-6-77 DO - 10.1186/1471-2148-6-77 ID - Cai2006 ER - TY - JOUR AU - Hansen, D. R. AU - Dastidar, S. G. AU - Cai, Z. AU - Penaflor, C. AU - Kuehl, J. V. AU - Boore, J. L. AU - Jansen, R. K. PY - 2007 DA - 2007// TI - Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium(Schisandraceae) JO - Mol Phylog Evol VL - 45 UR - https://doi.org/10.1016/j.ympev.2007.06.004 DO - 10.1016/j.ympev.2007.06.004 ID - Hansen2007 ER - TY - JOUR AU - Jansen, R. K. AU - Cai, Z. AU - Raubeson, L. A. AU - Daniell, H. AU - dePamphilis, C. W. AU - Leebens-Mack, J. AU - Muller, K. F. AU - Guisinger-Bellian, M. AU - Haberle, R. C. AU - Hansen, A. K. AU - Chumley, T. W. AU - Lee, S. -. B. AU - Peery, R. AU - McNeal, J. R. AU - Kuehl, J. V. AU - Boore, J. L. PY - 2007 DA - 2007// TI - Analysis of 81 genes from 64 chloroplast genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0709121104 DO - 10.1073/pnas.0709121104 ID - Jansen2007 ER - TY - JOUR AU - Strauss, S. H. AU - Palmer, J. D. AU - Howe, G. T. AU - Doerksen, A. H. PY - 1988 DA - 1988// TI - Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged JO - Proc Natl Acad Sci USA VL - 85 UR - https://doi.org/10.1073/pnas.85.11.3898 DO - 10.1073/pnas.85.11.3898 ID - Strauss1988 ER - TY - JOUR AU - Palmer, J. D. AU - Osorio, B. AU - Aldrich, J. AU - Thompson, W. F. PY - 1987 DA - 1987// TI - Chloroplast DNA evolution among legumes – loss of a large inverted repeat occurred prior to other sequence rearrangements JO - Curr Genet VL - 11 UR - https://doi.org/10.1007/BF00355401 DO - 10.1007/BF00355401 ID - Palmer1987 ER - TY - JOUR AU - Chumley, T. W. AU - Palmer, J. D. AU - Mower, J. P. AU - Fourcade, H. M. AU - Calie, P. J. AU - Boore, J. L. AU - Jansen, R. K. PY - 2006 DA - 2006// TI - The complete chloroplast genome sequence of Pelargonium x hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msl089 DO - 10.1093/molbev/msl089 ID - Chumley2006 ER - TY - JOUR AU - Wolfe, K. H. AU - Morden, C. W. AU - Palmer, J. D. PY - 1992 DA - 1992// TI - Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant JO - Proc Natl Acad Sci USA VL - 89 UR - https://doi.org/10.1073/pnas.89.22.10648 DO - 10.1073/pnas.89.22.10648 ID - Wolfe1992 ER - TY - JOUR AU - Raubeson, L. A. AU - Jansen, R. K. PY - 1992 DA - 1992// TI - Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants JO - Science VL - 255 UR - https://doi.org/10.1126/science.255.5052.1697 DO - 10.1126/science.255.5052.1697 ID - Raubeson1992 ER - TY - JOUR AU - Jansen, R. K. AU - Palmer, J. D. PY - 1987 DA - 1987// TI - A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae) JO - Proc Natl Acad Sci USA VL - 84 UR - https://doi.org/10.1073/pnas.84.16.5818 DO - 10.1073/pnas.84.16.5818 ID - Jansen1987 ER - TY - JOUR AU - Palmer, J. D. AU - Osorio, B. AU - Thompson, W. F. PY - 1988 DA - 1988// TI - Evolutionary significance of inversions in legume chloroplast DNAs JO - Curr Genet VL - 14 UR - https://doi.org/10.1007/BF00405856 DO - 10.1007/BF00405856 ID - Palmer1988 ER - TY - JOUR AU - Cosner, M. E. AU - Jansen, R. K. AU - Palmer, J. D. AU - Downie, S. R. PY - 1997 DA - 1997// TI - The highly rearranged chloroplast genome of Trachelium caeruleum(Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families JO - Curr Genet VL - 31 UR - https://doi.org/10.1007/s002940050225 DO - 10.1007/s002940050225 ID - Cosner1997 ER - TY - JOUR AU - Cosner, M. E. AU - Raubeson, L. A. AU - Jansen, R. K. PY - 2004 DA - 2004// TI - Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes JO - BMC Evol Biol VL - 4 UR - https://doi.org/10.1186/1471-2148-4-27 DO - 10.1186/1471-2148-4-27 ID - Cosner2004 ER - TY - JOUR AU - Lee, H. L. AU - Jansen, R. K. AU - Chumley, T. W. AU - Kim, K. J. PY - 2007 DA - 2007// TI - Gene relocations within chloroplast genomes of Jasminum and Menodora(Oleaceae) are due to multiple, overlapping inversions JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm036 DO - 10.1093/molbev/msm036 ID - Lee2007 ER - TY - JOUR AU - Clegg, M. T. AU - Gaut, B. S. AU - Learn, G. H. AU - Morton, B. R. PY - 1994 DA - 1994// TI - Rates and patterns of chloroplast DNA evolution JO - Proc Natl Acad Sci USA VL - 91 UR - https://doi.org/10.1073/pnas.91.15.6795 DO - 10.1073/pnas.91.15.6795 ID - Clegg1994 ER - TY - JOUR AU - Gaut, B. S. AU - Muse, S. V. AU - Clegg, M. T. PY - 1993 DA - 1993// TI - Relative rates of nucleotide substitution in the chloroplast genome JO - Mol Phylogenet Evol VL - 2 UR - https://doi.org/10.1006/mpev.1993.1009 DO - 10.1006/mpev.1993.1009 ID - Gaut1993 ER - TY - JOUR AU - Gaut, B. S. AU - Morton, B. R. AU - McCaig, B. C. AU - Clegg, M. T. PY - 1996 DA - 1996// TI - Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL JO - Proc Natl Acad Sci USA VL - 93 UR - https://doi.org/10.1073/pnas.93.19.10274 DO - 10.1073/pnas.93.19.10274 ID - Gaut1996 ER - TY - JOUR AU - Chang, C. C. AU - Lin, H. C. AU - Lin, I. P. AU - Chow, T. Y. AU - Chen, H. H. AU - Chen, W. H. AU - Cheng, C. H. AU - Lin, C. Y. AU - Liu, S. M. AU - Chang, C. C. AU - Chaw, S. M. PY - 2006 DA - 2006// TI - The chloroplast genome of Phalaenopsis aphrodite(Orchidaceae): Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj029 DO - 10.1093/molbev/msj029 ID - Chang2006 ER - TY - CHAP AU - Raubeson, L. A. AU - Jansen, R. K. ED - Henry, R. J. PY - 2005 DA - 2005// TI - Chloroplast genomes of plants BT - Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants UR - https://doi.org/10.1079/9780851999043.0045 DO - 10.1079/9780851999043.0045 ID - Raubeson2005 ER - TY - JOUR AU - Turmel, M. AU - Otis, C. AU - Lemieux, C. PY - 1999 DA - 1999// TI - The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.18.10248 DO - 10.1073/pnas.96.18.10248 ID - Turmel1999 ER - TY - JOUR AU - Tsudzuki, J. AU - Nakashima, K. AU - Tsudzuki, T. AU - Hiratsuka, J. AU - Shibata, M. AU - Wakasugi, T. AU - Sugiura, M. PY - 1992 DA - 1992// TI - Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16 JO - Mol Gen Genet VL - 232 ID - Tsudzuki1992 ER - TY - JOUR AU - Raubeson, L. A. PY - 1998 DA - 1998// TI - Chloroplast DNA structural similarities shared by conifers and Gnetales: coincidence or common ancestry? [abstract] JO - Am J Bot VL - 85 UR - https://doi.org/10.2307/2446303 DO - 10.2307/2446303 ID - Raubeson1998 ER - TY - JOUR AU - Perry, A. S. AU - Wolfe, K. H. PY - 2002 DA - 2002// TI - Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat JO - J Mol Evol VL - 55 UR - https://doi.org/10.1007/s00239-002-2333-y DO - 10.1007/s00239-002-2333-y ID - Perry2002 ER - TY - JOUR AU - Wolfe, K. H. AU - Morden, C. W. AU - Palmer, J. D. PY - 1992 DA - 1992// TI - Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant JO - Proc Natl Acad Sci USA VL - 89 UR - https://doi.org/10.1073/pnas.89.22.10648 DO - 10.1073/pnas.89.22.10648 ID - Wolfe1992 ER - TY - JOUR AU - Martin, W. AU - Rujan, T. AU - Richly, E. AU - Hansen, A. AU - Cornelsen, S. AU - Lins, T. AU - Leister, D. AU - Stoebe, B. AU - Hasegawa, M. AU - Penny, D. PY - 2002 DA - 2002// TI - Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.182432999 DO - 10.1073/pnas.182432999 ID - Martin2002 ER - TY - JOUR AU - Burke, D. H. AU - Raubeson, L. A. AU - Alberti, M. AU - Hearst, J. AU - Jordon, E. T. AU - Kirsch, S. AU - Conant, D. S. AU - Valinski, A. E. C. AU - Stein, D. B. PY - 1993 DA - 1993// TI - The chlL (frxC) Gene – Phylogenetic distribution in vascular plants and DNA sequence from Polystichum acrostichoides(Pteridophyta) and Synechococcus pp 7002 (Cyanobacteria) JO - Plant Syst Evol VL - 187 UR - https://doi.org/10.1007/BF00994092 DO - 10.1007/BF00994092 ID - Burke1993 ER - TY - JOUR AU - Thomas, F. AU - Massenet, O. AU - Dorne, A. M. AU - Briat, J. F. AU - Mache, R. PY - 1988 DA - 1988// TI - Expression of the rpl23, rpl2, and rps19 gene in spinach chloroplasts JO - Nucl Acids Res VL - 25 UR - https://doi.org/10.1093/nar/16.6.2461 DO - 10.1093/nar/16.6.2461 ID - Thomas1988 ER - TY - JOUR AU - Schmitz-Linneweber, C. AU - Maier, R. M. AU - Alcaraz, J. P. AU - Cottet, A. AU - Herrmann, R. G. AU - Mache, R. PY - 2001 DA - 2001// TI - The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization JO - Plt Mol Biol VL - 45 UR - https://doi.org/10.1023/A:1006478403810 DO - 10.1023/A:1006478403810 ID - Schmitz-Linneweber2001 ER - TY - JOUR AU - Doyle, J. J. AU - Doyle, J. L. AU - Palmer, J. D. PY - 1995 DA - 1995// TI - Multiple independent losses of two genes and one intron from legume chloroplast genomes JO - Syst Bot VL - 20 UR - https://doi.org/10.2307/2419496 DO - 10.2307/2419496 ID - Doyle1995 ER - TY - JOUR AU - Ohyama, K. PY - 1996 DA - 1996// TI - Chloroplast and mitochondrial genomes from a liverwort, Marchantia polymorpha– gene organization and molecular evolution JO - Bioscience Biotechnology and Biochemistry VL - 60 UR - https://doi.org/10.1271/bbb.60.16 DO - 10.1271/bbb.60.16 ID - Ohyama1996 ER - TY - JOUR AU - Hajibabaei, M. AU - Xia, J. AU - Drouin, G. PY - 2006 DA - 2006// TI - Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae JO - Mol Phylogenet Evol VL - 40 UR - https://doi.org/10.1016/j.ympev.2006.03.006 DO - 10.1016/j.ympev.2006.03.006 ID - Hajibabaei2006 ER - TY - JOUR AU - Martin, W. AU - Stoebe, B. AU - Goremykin, V. AU - Hansmann, S. AU - Hasegawa, M. AU - Kowallik, K. V. PY - 1998 DA - 1998// TI - Gene transfer to the nucleus and the evolution of chloroplasts JO - Nature VL - 393 UR - https://doi.org/10.1038/30234 DO - 10.1038/30234 ID - Martin1998 ER - TY - JOUR AU - Cantino, P. D. AU - Doyle, J. A. AU - Graham, S. W. AU - Judd, W. S. AU - Olmstead, R. G. AU - Soltis, D. E. AU - Soltis, P. S. AU - Donoghue, M. J. PY - 2007 DA - 2007// TI - Towards a phylogenetic nomenclature of Tracheophyta JO - Taxon VL - 56 UR - https://doi.org/10.2307/25065865 DO - 10.2307/25065865 ID - Cantino2007 ER - TY - JOUR AU - Graham, S. W. AU - Olmstead, R. G. PY - 2000 DA - 2000// TI - Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms JO - Am J Bot VL - 87 UR - https://doi.org/10.2307/2656749 DO - 10.2307/2656749 ID - Graham2000 ER - TY - JOUR AU - Chaw, S. M. AU - Parkinson, C. L. AU - Cheng, Y. C. AU - Vincent, T. M. AU - Palmer, J. D. PY - 2000 DA - 2000// TI - Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.97.8.4086 DO - 10.1073/pnas.97.8.4086 ID - Chaw2000 ER - TY - JOUR AU - Sanderson, M. J. AU - Wojciechowski, M. F. AU - Hu, J. M. AU - Khan, T. S. AU - Brady, S. G. PY - 2000 DA - 2000// TI - Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026357 DO - 10.1093/oxfordjournals.molbev.a026357 ID - Sanderson2000 ER - TY - JOUR AU - Sanderson, M. J. PY - 2002 DA - 2002// TI - Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003974 DO - 10.1093/oxfordjournals.molbev.a003974 ID - Sanderson2002 ER - TY - JOUR AU - Mindell, D. P. AU - Thacker, C. E. PY - 1996 DA - 1996// TI - Rates of Molecular Evolution: Phylogenetic Issues and Applications JO - Ann Rev Ecol Syst VL - 27 UR - https://doi.org/10.1146/annurev.ecolsys.27.1.279 DO - 10.1146/annurev.ecolsys.27.1.279 ID - Mindell1996 ER - TY - JOUR AU - Jansen, R. K. AU - Raubeson, L. A. AU - Boore, J. L. AU - dePamphilis, C. W. AU - Chumley, T. W. AU - Haberle, R. C. AU - Wyman, S. K. AU - Alverson, A. J. AU - Peery, R. AU - Herman, S. J. AU - Fourcade, H. M. AU - Kuehl, J. V. AU - McNeal, J. R. AU - Leebens-Mack, J. AU - Cui, L. PY - 2005 DA - 2005// TI - Methods for obtaining and analyzing whole chloroplast genome sequences JO - Methods Enzymol VL - 395 UR - https://doi.org/10.1016/S0076-6879(05)95020-9 DO - 10.1016/S0076-6879(05)95020-9 ID - Jansen2005 ER - TY - STD TI - JGI – Protocols in Production Sequencing. [http://www.jgi.doe.gov/sequencing/protocols/prots_production.html] UR - http://www.jgi.doe.gov/sequencing/protocols/prots_production.html ID - ref67 ER - TY - JOUR AU - Gordon, D. AU - Abajian, C. AU - Green, P. PY - 1998 DA - 1998// TI - Consed: A graphical tool for sequence finishing JO - Genome Res VL - 8 UR - https://doi.org/10.1101/gr.8.3.195 DO - 10.1101/gr.8.3.195 ID - Gordon1998 ER - TY - JOUR AU - Ewing, B. AU - Green, P. PY - 1998 DA - 1998// TI - Base-calling of automated sequencer traces using phred. II. Error probabilities JO - Genome Res VL - 8 UR - https://doi.org/10.1101/gr.8.3.186 DO - 10.1101/gr.8.3.186 ID - Ewing1998 ER - TY - JOUR AU - Wyman, S. K. AU - Jansen, R. K. AU - Boore, J. L. PY - 2004 DA - 2004// TI - Automatic annotation of organellar genomes with DOGMA JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth352 DO - 10.1093/bioinformatics/bth352 ID - Wyman2004 ER - TY - STD TI - DOGMA (Dual Organellar Genome Annotator). [http://dogma.ccbb.utexas.edu/] UR - http://dogma.ccbb.utexas.edu/ ID - ref71 ER - TY - STD TI - BLAST (Basic Local Alignment Tool). [http://www.ncbi.nlm.nih.gov/BLAST/] UR - http://www.ncbi.nlm.nih.gov/BLAST/ ID - ref72 ER - TY - STD TI - ORF Finder. [http://www.ncbi.nlm.nih.gov/gorf/gorf.html] UR - http://www.ncbi.nlm.nih.gov/gorf/gorf.html ID - ref73 ER - TY - JOUR AU - Schwartz, S. AU - Zhang, Z. AU - Frazer, K. A. AU - Smit, A. AU - Riemer, C. AU - Bouck, J. AU - Gibbs, R. AU - Hardison, R. AU - Miller, W. PY - 2000 DA - 2000// TI - PipMaker – A Web server for aligning two genomic DNA sequences JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.10.4.577 DO - 10.1101/gr.10.4.577 ID - Schwartz2000 ER - TY - JOUR AU - Tesler, G. PY - 2002 DA - 2002// TI - GRIMM: genome rearrangements web server JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.492 DO - 10.1093/bioinformatics/18.3.492 ID - Tesler2002 ER - TY - STD TI - GRIMM – Genome rearrangement algorithms. [http://nbcr.sdsc.edu/GRIMM/mgr.cgi] UR - http://nbcr.sdsc.edu/GRIMM/mgr.cgi ID - ref76 ER - TY - JOUR AU - Kumar, S. AU - Tamura, K. AU - Nei, M. PY - 2004 DA - 2004// TI - MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment JO - Brief Bioinform VL - 5 UR - https://doi.org/10.1093/bib/5.2.150 DO - 10.1093/bib/5.2.150 ID - Kumar2004 ER - TY - JOUR AU - Tamura, K. AU - Dudley, J. AU - Nei, M. AU - Kumar, S. PY - 2007 DA - 2007// TI - MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0 JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm092 DO - 10.1093/molbev/msm092 ID - Tamura2007 ER - TY - JOUR AU - Leebens-Mack, J. AU - Raubeson, L. A. AU - Cui, L. AU - Kuehl, J. AU - Fourcade, M. AU - Chumley, T. AU - Boore, J. L. AU - Jansen, R. K. AU - dePamphilis, C. W. PY - 2005 DA - 2005// TI - Identifying the basal angiosperms in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi191 DO - 10.1093/molbev/msi191 ID - Leebens-Mack2005 ER - TY - CHAP AU - Swofford, D. L. PY - 2003 DA - 2003// BT - PAUP*: Phylogenetic analysis using parsimony (* and other methods), ver. 4.0 PB - Sinauer Associates CY - Sunderland MA ID - Swofford2003 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Ronquist, F. PY - 2001 DA - 2001// TI - MRBAYES: Bayesian inference of phylogeny JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.754 DO - 10.1093/bioinformatics/17.8.754 ID - Huelsenbeck2001 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 1998 DA - 1998// TI - MODELTEST: testing the model of DNA substitution JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.9.817 DO - 10.1093/bioinformatics/14.9.817 ID - Posada1998 ER - TY - STD TI - Wilgenbusch JC, Warren DL, Swofford DL: AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. [http://ceb.csit.fsu.edu/awty] UR - http://ceb.csit.fsu.edu/awty ID - ref83 ER - TY - JOUR AU - Shimodaira, H. AU - Hasegawa, M. PY - 1999 DA - 1999// TI - Multiple comparisons of log-likelihoods with applications to phylogenetic inference JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026201 DO - 10.1093/oxfordjournals.molbev.a026201 ID - Shimodaira1999 ER -