TY - JOUR AU - Palmer, J. D. PY - 1985 DA - 1985// TI - Chloroplast DNA and molecular phylogeny JO - Bioessays VL - 2 UR - https://doi.org/10.1002/bies.950020607 DO - 10.1002/bies.950020607 ID - Palmer1985 ER - TY - JOUR AU - Maliga, P. PY - 2004 DA - 2004// TI - Plastid transformation in higher plants JO - Annu Rev Plant Biol VL - 55 UR - https://doi.org/10.1146/annurev.arplant.55.031903.141633 DO - 10.1146/annurev.arplant.55.031903.141633 ID - Maliga2004 ER - TY - JOUR AU - Grevich, J. J. AU - Daniell, H. PY - 2005 DA - 2005// TI - Chloroplast genetic engineering: Recent advances and future perspectives JO - Critical Reviews in Plant Sciences VL - 24 UR - https://doi.org/10.1080/07352680590935387 DO - 10.1080/07352680590935387 ID - Grevich2005 ER - TY - JOUR AU - Daniell, H. AU - Kumar, S. AU - Dufourmantel, N. PY - 2005 DA - 2005// TI - Breakthrough in chloroplast genetic engineering of agronomically important crops JO - Trends Biotechnol VL - 23 UR - https://doi.org/10.1016/j.tibtech.2005.03.008 DO - 10.1016/j.tibtech.2005.03.008 ID - Daniell2005 ER - TY - CHAP AU - Dhingra, A. AU - Daniell, H. ED - Salinas, J. ED - Sanchez-Serrano, J. J. PY - 2005 DA - 2005// TI - Chloroplast genetic engineering via organogenesis or somatic embryogenesis BT - Arabidopsis Protocols PB - Humana Press CY - Totowa, New Jersey ID - Dhingra2005 ER - TY - JOUR AU - Sato, S. AU - Nakamura, Y. AU - Kaneko, T. AU - Asamizu, E. AU - Tabata, S. PY - 1999 DA - 1999// TI - Complete structure of the chloroplast genome of Arabidopsis thaliana JO - DNA Res VL - 6 UR - https://doi.org/10.1093/dnares/6.5.283 DO - 10.1093/dnares/6.5.283 ID - Sato1999 ER - TY - JOUR AU - Schmitz-Linneweber, C. AU - Regel, R. AU - Du, T. G. AU - Hupfer, H. AU - Herrmann, R. G. AU - Maier, R. M. PY - 2002 DA - 2002// TI - The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004222 DO - 10.1093/oxfordjournals.molbev.a004222 ID - Schmitz-Linneweber2002 ER - TY - JOUR AU - Hiratsuka, J. AU - Shimada, H. AU - Whittier, R. AU - Ishibashi, T. AU - Sakamoto, M. AU - Mori, M. AU - Kondo, C. AU - Honji, Y. AU - Sun, C. R. AU - Meng, B. Y. PY - 1989 DA - 1989// TI - 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 JO - Mol Gen Genet VL - 217 UR - https://doi.org/10.1007/BF02464880 DO - 10.1007/BF02464880 ID - Hiratsuka1989 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 (Spinacea oleracea): complete nucleotide sequence and gene organization JO - Plant Mol Biol VL - 45 UR - https://doi.org/10.1023/A:1006478403810 DO - 10.1023/A:1006478403810 ID - Schmitz-Linneweber2001 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 - Yamaguchi-Shinozaki, 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 tobacco chloroplast genome:its gene organization and expression JO - EMBO J VL - 5 ID - Shinozaki1986 ER - TY - JOUR AU - Ogihara, Y. AU - Isono, K. AU - Kojima, T. AU - Endo, A. AU - Hanaoka, M. AU - Shiina, T. AU - Terachi, T. AU - Utsugi, S. AU - Murata, M. AU - Mori, N. AU - Takumi, S. AU - Ikeo, K. AU - Gojobori, T. AU - Murai, R. AU - Murai, K. AU - Matsuoka, Y. AU - Ohnishi, Y. AU - Tajiri, H. AU - Tsunewaki, K. PY - 2002 DA - 2002// TI - Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA JO - Mol Genet Genomics VL - 266 UR - https://doi.org/10.1007/s00438-001-0606-9 DO - 10.1007/s00438-001-0606-9 ID - Ogihara2002 ER - TY - CHAP AU - Kato, T. AU - Kaneko, T. AU - Sato, S. AU - Nakamura, Y. AU - Tabata, S. PY - 2000 DA - 2000// BT - Complete structure of the chloroplast genome of a legume, Lotus japonicus ID - Kato2000 ER - TY - JOUR AU - Maier, R. M. AU - Neckermann, K. AU - Igloi, G. L. AU - Kossel, H. PY - 1995 DA - 1995// TI - Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing JO - J Mol Biol VL - 251 UR - https://doi.org/10.1006/jmbi.1995.0460 DO - 10.1006/jmbi.1995.0460 ID - Maier1995 ER - TY - JOUR AU - Kim, K. J. AU - Lee, H. L. PY - 2004 DA - 2004// TI - Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants JO - DNA Res VL - 11 UR - https://doi.org/10.1093/dnares/11.4.247 DO - 10.1093/dnares/11.4.247 ID - Kim2004 ER - TY - CHAP AU - Saski, C. AU - Lee, S. B. AU - Daniell, H. AU - Wood, T. C. AU - Tomkins, J. AU - Kim, H. G. AU - Jansen, R. K. PY - 2005 DA - 2005// BT - Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes ID - Saski2005 ER - TY - JOUR AU - Asano, T. AU - Tsudzuki, T. AU - Takahashi, S. AU - Shimada, H. AU - Kadowaki, K. PY - 2004 DA - 2004// TI - Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes JO - DNA Res VL - 11 UR - https://doi.org/10.1093/dnares/11.2.93 DO - 10.1093/dnares/11.2.93 ID - Asano2004 ER - TY - JOUR AU - Soltis, D. E. AU - Albert, V. A. AU - Savolainen, V. AU - Hilu, K. AU - Qiu, Y. L. AU - Chase, M. W. AU - Farris, J. S. AU - Stefanovic, S. AU - Rice, D. W. AU - Palmer, J. D. AU - Soltis, P. S. PY - 2004 DA - 2004// TI - Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics JO - Trends in Plant Science VL - 9 UR - https://doi.org/10.1016/j.tplants.2004.08.008 DO - 10.1016/j.tplants.2004.08.008 ID - Soltis2004 ER - TY - JOUR AU - Wolf, P. G. AU - Rowe, C. A. AU - Sinclair, R. B. AU - Hasebe, M. PY - 2003 DA - 2003// TI - Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L JO - DNA Research VL - 10 UR - https://doi.org/10.1093/dnares/10.2.59 DO - 10.1093/dnares/10.2.59 ID - Wolf2003 ER - TY - JOUR AU - Martin, W. AU - Deusch, O. AU - Stawski, N. AU - Grunheit, N. AU - Goremykin, V. PY - 2005 DA - 2005// TI - Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution JO - Trends Plant Sci VL - 10 UR - https://doi.org/10.1016/j.tplants.2005.03.007 DO - 10.1016/j.tplants.2005.03.007 ID - Martin2005 ER - TY - STD TI - Project DT: . [http://www.flmnh.ufl.edu/deeptime/] UR - http://www.flmnh.ufl.edu/deeptime/ ID - ref20 ER - TY - STD TI - Project CGS: . [http://www.genome.clemson.edu/projects/Chloroplast/] UR - http://www.genome.clemson.edu/projects/Chloroplast/ ID - ref21 ER - TY - STD TI - project C: . [http://evogen.jgi.doe.gov/second_levels/chloroplasts/jansen_project_home/chlorosite.html] UR - http://evogen.jgi.doe.gov/second_levels/chloroplasts/jansen_project_home/chlorosite.html ID - ref22 ER - TY - JOUR AU - Wolf, P. G. AU - Karol, K. G. AU - Mandoli, D. F. AU - Kuehl, J. AU - Arumuganathan, K. AU - Ellis, M. W. AU - Mishler, B. D. AU - Kelch, D. G. AU - Olmstead, R. G. AU - Boore, J. L. PY - 2005 DA - 2005// TI - The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae) JO - Gene VL - 350 UR - https://doi.org/10.1016/j.gene.2005.01.018 DO - 10.1016/j.gene.2005.01.018 ID - Wolf2005 ER - TY - STD TI - Website D: . [http://bugmaster.jgi-psf.org/dogma/] UR - http://bugmaster.jgi-psf.org/dogma/ ID - ref24 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 - JOUR AU - Palmer, J. D. PY - 1985 DA - 1985// TI - Comparative organization of chloroplast genomes JO - Annu Rev Genet VL - 19 UR - https://doi.org/10.1146/annurev.ge.19.120185.001545 DO - 10.1146/annurev.ge.19.120185.001545 ID - Palmer1985 ER - TY - JOUR AU - Odintsova, M. S. AU - Iurina, N. P. PY - 2003 DA - 2003// TI - Plastidic genome of higher plants and algae: structure and function JO - Mol Biol (Mosk) VL - 37 UR - https://doi.org/10.1023/A:1026020623631 DO - 10.1023/A:1026020623631 ID - Odintsova2003 ER - TY - CHAP 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. PY - 2005 DA - 2005// TI - Methods for obtaining and analyzing whole chloroplast genome sequences BT - Methods in Enzymology ID - Jansen2005 ER - TY - JOUR AU - Folta, K. M. AU - Staton, M. AU - Stewart, P. J. AU - Jung, S. AU - Bies, D. H. AU - Jesudurai, C. AU - Main, D. PY - 2005 DA - 2005// TI - Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria x ananassa) JO - BMC Plant Biol VL - 5 UR - https://doi.org/10.1186/1471-2229-5-12 DO - 10.1186/1471-2229-5-12 ID - Folta2005 ER - TY - JOUR AU - Lin, J. AU - Davis, T. M. PY - 2000 DA - 2000// TI - S1 analysis of long PCR heteroduplexes: detection of chloroplast indel polymorphisms in Fragaria JO - Theoretical and Applied Genetics VL - 101 UR - https://doi.org/10.1007/s001220051498 DO - 10.1007/s001220051498 ID - Lin2000 ER - TY - JOUR AU - Kumar, S. AU - Dhingra, A. AU - Daniell, H. PY - 2004 DA - 2004// TI - Plastid-expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots, and leaves confers enhanced salt tolerance JO - Plant Physiology VL - 136 UR - https://doi.org/10.1104/pp.104.045187 DO - 10.1104/pp.104.045187 ID - Kumar2004 ER - TY - JOUR AU - Kumar, S. AU - Dhingra, A. AU - Daniell, H. PY - 2004 DA - 2004// TI - Stable transformation of the cotton plastid genome and maternal inheritance of transgenes JO - Plant Molecular Biology VL - 56 UR - https://doi.org/10.1007/s11103-004-2907-y DO - 10.1007/s11103-004-2907-y ID - Kumar2004 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 - 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 Amborella is 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 - Matsuo, M. AU - Ito, Y. AU - Yamauchi, R. AU - Obokata, J. PY - 2005 DA - 2005// TI - The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.104.027706 DO - 10.1105/tpc.104.027706 ID - Matsuo2005 ER - TY - STD TI - website CW: . [http://www.ebi.ac.uk/clustalw/] UR - http://www.ebi.ac.uk/clustalw/ ID - ref36 ER - TY - JOUR AU - Demeke, T. AU - Adams, R. P. PY - 1992 DA - 1992// TI - The effects of plant polysaccharides and buffer additives on PCR JO - Biotechniques VL - 12 ID - Demeke1992 ER - TY - JOUR AU - Don, R. H. AU - Cox, P. T. AU - Wainwright, B. J. AU - Baker, K. AU - Mattick, J. S. PY - 1991 DA - 1991// TI - Touchdown PCR to circumvent spurious priming during gene amplification JO - Nucleic Acids Research VL - 19 UR - https://doi.org/10.1093/nar/19.14.4008 DO - 10.1093/nar/19.14.4008 ID - Don1991 ER - TY - STD TI - . [http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi] UR - http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi ID - ref39 ER - TY - JOUR AU - Tatusova, T. A. AU - Madden, T. L. PY - 1999 DA - 1999// TI - BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences JO - Fems Microbiology Letters VL - 174 UR - https://doi.org/10.1111/j.1574-6968.1999.tb13575.x DO - 10.1111/j.1574-6968.1999.tb13575.x ID - Tatusova1999 ER - TY - JOUR AU - Huang, X. Q. AU - Madan, A. PY - 1999 DA - 1999// TI - CAP3: A DNA sequence assembly program JO - Genome Research VL - 9 UR - https://doi.org/10.1101/gr.9.9.868 DO - 10.1101/gr.9.9.868 ID - Huang1999 ER - TY - STD TI - Huang XQ, Madan A: . [http://genome.cs.mtu.edu/cap/cap3.html] UR - http://genome.cs.mtu.edu/cap/cap3.html ID - ref42 ER -