Abstract
Plant cells possess two more genomes besides the central nuclear genome: the mitochondrial genome and the chloroplast genome (or plastome). Compared to the gigantic nuclear genome, these organelle genomes are tiny and are present in high copy number. These genomes are less prone to recombination and, therefore, retain signatures of their age to a much better extent than their nuclear counterparts. Thus, they are valuable phylogenetic tools, giving useful information about the relative age and relatedness of the organisms possessing them. Unlike animal cells, mitochondrial genomes of plant cells are characterized by large size, extensive intramolecular recombination and low nucleotide substitution rates and are of limited phylogenetic utility. Chloroplast genomes, on the other hand, show resemblance to animal mitochondrial genomes in terms of phylogenetic utility and are more relevant and useful in case of plants. Conservation in gene order, content and lack of recombination make the plastome an attractive tool for plant phylogenetic studies. Their importance is reflected in the rapid increase in the availability of complete chloroplast genomes in the public databases. This review aims to summarize the progress in chloroplast genome research since its inception and tries to encompass all related aspects. Starting with a brief historical account, it gives a detailed account of the current status of chloroplast genome sequencing and touches upon RNA editing, ycfs, molecular phylogeny, DNA barcoding as well as gene transfer to the nucleus.
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Allen JF (2003). The function of genomes in bioenergetic organelles. Philos Trans Roy Soc Lond B Biol Sci 358: 19–37
Archibald JM (2005). Jumping genes and shrinking genomes – probing the evolution of eukaryotic photosynthesis with genomics. IUBMB Life 57: 539–547
Asano T, Tsudzuki T, Takahashi S, Shimada H and Kadowaki K (2004). Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res 11: 93–99
Bausher MG, Singh ND, Lee SB, Jansen RK and Daniell H (2006). The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var `Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Pl Biol 6: 21
Bedbrook JR and Bogorad L (1976). Endonuclease recognition sites mapped on Zea mays chloroplast DNA. Proc Natl Acad Sci USA 73: 4309–4313
Belanger AS, Brouard JS, Charlebois P, Otis C, Lemieux C, Turmel M (2006) Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum. Molec Genet Genomics 276: 464–477
Bendich AJ (2004). Circular chloroplast chromosomes: the grand illusion. Pl Cell 16: 1661–1666
Boudreau E, Takahashi Y, Lemieux C, Turmel M and Rochaix JD (1997). The chloroplast ycf3 and ycf4 open reading frames of Chlamydomonas reinhardtii are required for the accumulation of the photosystem I complex. EMBO J 16: 6095–6104
Brennicke A, Grohmann L, Hiesel R, Knoop V and Schuster W (1993). The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Lett 325: 140–145
Brocks JJ, Logan GA, Buick R and Summons RE (1999). Archean molecular fossils and the early rise of eukaryotes. Science 285: 1033–1036
Butterfield NJ (2000). Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26: 386–404
Cai X, Fuller AL, McDougald LR and Zhu G (2003). Apicoplast genome of the coccidian Eimeria tenella. Gene 321: 39–46
Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL and Jansen R K (2006). Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 6: 77
Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chang CC and 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: 279–291
Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N and Savolainen V (2005). Land plants and DNA barcodes: short-term and long-term goals. Philos Trans Roy Soc Lond, B, Biol Sci 360: 1889–1895
Chiba Y (1951). Cytochemical studies on chloroplasts I. Cytologic demonstration of nucleic acids in chloroplasts. Cytologia (Tokyo) 16: 259–264
Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL and Jansen RK (2006). The complete chloroplast genome sequence of Pelargonium × hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molec Biol Evol 23: 2175–2190
Cui L, Veeraraghavan N, Richter A, Wall K, Jansen R K, Leebens-Mack J, Makalowska I and dePamphilis C W (2006). ChloroplastDB: the chloroplast genome database. Nuclic Acids Res 34: D692–D696
Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen RK (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112: 1503–1518
Otis C, Lemieux C, Turmel M and Cambiaire JC (2006). The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands. BMC Evol Biol 6: 37
Keeling PJ and Koning AP (2006). The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured. BMC Biol 4: 12
Douglas SE and Penny SL (1999). The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. J Molec Evol 48: 236–244
Doyle JJ, Davis JI, Soreng RJ, Garvin D and Anderson M J (1992). Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proc Natl Acad Sci USA 89: 7722–7726
Drescher A, Ruf S, Carrer H, Bock R and Calsa T (2000). The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Pl J 22: 97–104
Embley TM and Martin W (2006). Eukaryotic evolution, changes and challenges. Nature 440: 623–630
Gardner MJ, Bishop R, Shah T, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson R J, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V and Villiers EP (2005). Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309: 134–137
Gargano D, Vezzi A, Scotti N, Gray JC, Valle G, Grillo S, Cardi T (2005) The complete nucleotide sequence of potato (Solanum tuberosum cv. Desiree) chloroplast DNA In: Abstracts of the 2nd Solanaceae Genome Workshop 2005: 107
Glöckner G, Rosenthal A and Valentin K (2000). The structure and gene repertoire of an ancient red algal plastid genome. J Molec Evol 51: 382–390
Gockel G and Hachtel W (2000). Complete gene map of the plastid genome of the nonphotosynthetic euglenoid flagellate Astasia longa. Protist 151: 347–351
Goremykin VV, Hansmann S and Martin WF (1997). Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: Revised molecular estimates of two seed plant divergence times. Pl Syst Evol 206: 337–351
Goremykin VV, Hirsch-Ernst KI, Wolfl S and Hellwig FH (2003a). The chloroplast genome of the `basal' angiosperm Calycanthus fertilis – structural and phylogenetic analysis. Pl Syst Evol 242: 119–135
Goremykin VV, Hirsch-Ernst KI, Wolfl S and Hellwig FH (2003b). Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Molec Biol Evol 20: 1499–1505
Goremykin VV, Hirsch-Ernst KI, Wolfl S and Hellwig FH (2004). The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Molec Biol Evol 21: 1445–1454
Goremykin VV, Holland B, Hirsch-Ernst KI and Hellwig FH (2005). Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Molec Biol Evol 22: 1813–1822
Goulding SE, Olmstead RG, Morden CW and Wolfe KH (1996). Ebb and flow of the chloroplast inverted repeat. Molec Gen Genet 252: 195–206
Hager M, Biehler K, Illerhaus J, Ruf S and Bock R (1999). Targeted inactivation of the smallest plastid genome-encoded open reading frame reveals a novel and essential subunit of the cytochrome b(6)f complex. EMBO J 18: 5834–5842
Hagopian JC, Reis M, Kitajima JP, Bhattacharya D and Oliveira MC (2004). Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. J Molec Evol 59: 464–477
Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95–98
Hallick RB and Bairoch A (1994). Proposal for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes. Pl Molec Biol Rep 12: S29–S30
Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A, Orsat B, Spielmann A and Stutz E (1993). Complete sequence of Euglena gracilis chloroplast DNA. Nucl Acids Res 21: 3537–3544
Hebert PD, Cywinska A, Ball SL and deWaard JR (2003). Biological identifications through DNA barcodes. Proc Roy Soc Lond B Biol Sci 270: 313–321
Hebert PD and Gregory TR (2005). The promise of DNA barcoding for taxonomy. Syst Biol 54: 852–859
Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun C-R, Meng B-Y, Li Y-Q, Kanno A, Nishizawa Y, Hirai A, Shinozaki K and Sugiura M (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. Molec Gen Genet 217: 185–194
Hirose T, Kusumegi T, Tsudzuki T and Sugiura M (1999). RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity. Molec Gen Genet 262: 462–467
Huang CY, Grünheit N, Ahmadinejad N, Timmis JN and Martin W (2005). Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Pl Physiol 138: 1723–1733
Hupfer H, Swiatek M, Hornung S, Herrmann RG, Maier RM, Chiu WL and Sears B (2000). Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes. Molec Gen Genet 263: 581–585
Jansen RK, Kaittanis C, Lee S B, Saski C, Tomkins J, Alverson AJ and Daniell H (2006). Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6: 32
Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J and Cui L (2005). Methods for obtaining and analyzing whole chloroplast genome sequences. Meth Enzymol 395: 348–384
Jarvis P and Soll J (2001). Toc, Tic and chloroplast protein import. Biochim Biophys Acta 1541: 64–79
Kahlau S, Aspinall S, Gray JC and Bock R (2006). Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J Molec Evol 63: 194–207
Källersjö M, Farris JS, Chase MW, Bremer B, Fay MF, Humphries CJ, Petersen G, Seberg O and Bremer K (1998). Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl Syst Evol 213: 259–287
Kato T, Kaneko T, Sato S, Nakamura Y and Tabata S (2000). Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res 7: 323–330
Kim J-S, Jung JD, Lee J-A, Park H-W, Oh K-H, Jeong WJ, Choi DW, Liu JR and Cho KY (2006). Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Pl Cell Rep 25: 334–340
Kim KJ and Lee HL (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
Kostianovsky M (2000). Evolutionary origin of eukaryotic cells. Ultrastruct Pathol 24: 59–66
Kowallik KV, Stoebe B, Schaffran I, Kroth-Pancic P and Freier U (1995). The chloroplast genome of a chlorophyll a + c-containing alga, Odontella sinensis. Pl Molec Biol Rep 13: 336–342
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA and Janzen DH (2005). Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102: 8369–8374
Kugita M, Kaneko A, Yamamoto Y, Takeya Y, Matsumoto T and Yoshinaga K (2003a). The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucl Acids Res 31: 716–721
Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T and Yoshinaga K (2003b). RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucl Acids Res 31: 2417–2423
Kumar S, Tamura K and Nei M (2004). MEGA3: integrated software for molecular evolutionary analysis and sequence alignment. Brief Bioinf 5: 150–163
Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD and Daniell H (2006). The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7: 61
Leister D (2003). Chloroplast research in the genomic age. Trends Genet 19: 47–56
Lemieux C, Otis C and Turmel M (2000). Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 403: 649–652
Lockhart PJ and Penny D (2005). The place of Amborella within the radiation of angiosperms. Trends Pl Sci 10: 201–202
Mäenpää P, Gonzalez EB, Chen L, Khan MS, Gray JC and Aro EM (2000). The ycf9 (orf 62) gene in the plant chloroplast genome encodes a hydrophobic protein of stromal thylakoid membranes. J Exp Bot 51: 375–382
Maier RM, Neckermann K, Igloi GL and Kossel H (1995). Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Molec Biol 251: 614–628
Manning JE, Wolstenholme DR, Ryan RS, Hunter JA and Richards OC (1971). Circular chloroplast DNA from Euglena gracilis. Proc Natl Acad Sci USA 68: 1169–1173
Margulis L (1970). Origin of Eukaryotic Cells. Yale University Press, New Haven
Martin W, Deusch O, Stawski N, Grunheit N and Goremykin V (2005). Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Pl Sci 10: 203–209
Martin W and Herrmann RG (1998). Gene transfer from organelles to the nucleus: how much, what happens and why?. Pl Physiol 118: 9–17
Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M and Penny D (2002). Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 99: 12246–12251
Martin W, Stoebe B, Goremykin V, Hapsmann S, Hasegawa M and Kowallik K V (1998). Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393: 162–165
Matsuo M, Ito Y, Yamauchi R and Obokata J (2005). The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. Pl Cell 17: 665–675
Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH and Stern DB (2002). The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Pl Cell 14: 2659–2679
Mereschkowsky C (1905) Über Natur und Ursprung der Chromatophoren im Pflanzenreiche. Biol. Centralbl. 25:593–604. English translation. In: Martin W, Kowallik KV (1999) Annotated English translation of Mereschkowsky's 1905 paper ``Über Natur und Ursprung der Chromatophoren im Pflanzenreiche''. Eur J Phycol 34: 287–295
Monod C, Takahashi Y, Goldschmidt-Clermont M and Rochaix JD (1994). The chloroplast ycf8 open reading frame encodes a photosystem II polypeptide which maintains photosynthetic activity under adverse growth conditions. EMBO J 13: 2747–2754
Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM and Soltis DE (2006). Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Pl Biol 6: 17
Newmaster SG, Fazekas AJ and Ragupathy S (2006). DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canad J Bot 84: 335–341
O'Brien EA, Zhang Y, Yang LS, Wang E, Marie V, Lang BF and Burger G (2006). GOBASE - a database of organelle and bacterial genome information. Nucl Acids Res 34: D697–D699
Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H and Tsunewaki K (2002). Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Molec Genet Genomics 266: 740–746
Ohta N, Matsuzaki M, Misumi O, Miyagishima S Y, Nozaki H, Tanaka K, Shin-I T, Kohara Y and Kuroiwa T (2003). Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Res 10: 67–77
Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S-I, Inokuchi H and Ozeki H (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322: 572–574
Palmer JD, Nugent JM and Herbon LA (1987). Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proc Natl Acad Sci USA 84: 769–773
Perry AS and Wolfe KH (2002). Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. J Molec Evol 55: 501–508
Pombert JF, Otis C, Lemieux C and Turmel M (2005). The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of Chlorophyte lineages. Molec Biol Evol 22: 1903–1918
Race HL, Herrmann RG and Martin W (1999). Why have organelles retained genomes?. Trends Genet 15: 364–370
Ravi V, Khurana JP, Tyagi AK and Khurana P (2006). The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet Genomes 3: 49–59
Ravi V, Khurana JP, Tyagi AK and Khurana P (2007). Rosales sister to Fabales: towards resolving the rozid puzzle. Molec Phylogenet Evol 44: 488–493
Reith ME and Munholland J (1995). Complete nucleotide sequence of Porphyra purpurea chloroplast genome. Pl Molec Biol Rep 13: 333–335
Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y (2007) The chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Molec Biol Evol 24: 956–968
Rogers MB, Gilson PR, Su V, McFadden GI and Keeling PJ (2007). The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Molec Biol Evol 24: 54–62
Rolland N, Dorne AJ, Amoroso G, Sültemeyer D, Joyard J and Rochaix JD (1997). Disruption of the plastid ycf10 open reading frame affects uptake of inorganic carbon in the chloroplasts of Chlamydomonas. EMBO J 16: 6713–6726
Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD and Daniell H (2006). Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7: 222
Sager R and Ishida MR (1963). Chloroplast DNA in Chlamydomonas. Proc Natl Acad Sci USA 50: 725–730
Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H (2007) The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. Pl Biotech J 5: 339–353
Sanchez H, Fester T, Kloska S, Schroder W and Schuster W (1996). Transfer of rps19 to the nucleus involves the gain of an RNP-binding motif which may functionally replace RPS13 in Arabidopsis mitochondria. EMBO J 15: 2138–2149
Sánchez Puerta MV, Bachvaroff TR and Delwiche CF (2005). The complete plastid genome sequence of the haptophyte Emiliania huxleyi: a comparison to other plastid genomes. DNA Res 12: 151–156
Sanderson MJ and Driskell AC (2003). The challenge of constructing large phylogenetic trees. Trends Pl Sci 8: 374–379
Saski C, Lee S-B, Daniell H, Wood TC, Tomkins J, Kim HG and Jansen RK (2005). Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Pl Molec Biol 59: 309–322
Sato S, Nakamura Y, Kaneko T, Asamizu E and Tabata S (1999). Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6: 283–290
Saunders GW (2005) Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans Roy Soc Lond B Biol Sci 360: 1879–1888
Schimper AFW (1883) Über die Entwicklung der Chlorophyllkörner und Farbkörper. Bot. Zeitung 41: 105–114, 121–131, 137–146, 153–162
Schmitz-Linneweber C, Maier RM, Alcaraz JP, Cottet A, Herrmann RG and Mache R (2001). The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Pl Molec Biol 45: 307–315
Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG and Maier RM (2002). 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 speciation. Molec Biol Evol 19: 1602–1612
Shahid Masood M, Nishikawa T, Fukuoka S, Njenga PK, Tsudzuki T and Kadowaki K-I (2004). The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 340: 133–139
Shahmuradov IA, Akbarova YY, Solovyev VV and Aliyev JA (2003). Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Pl Molec Biol 52: 923–934
Shimada H and Sugiura M (1991). Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucl Acids Res 19: 983–995
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H and Sugiura M (1986). The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5: 2043–2049
Soltis DE, Albert VA, Savolainen V, Hilu K, Qiu YL, Chase MW, Farris JS, Stefanovic S, Rice DW, Palmer JD and Soltis PS (2004). Genome-scale data, angiosperm relationships, and ``ending incongruence'': a cautionary tale in phylogenetics. Trends Pl Sci 9: 477–483
Steane DA (2005). Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res 12: 215–220
Stefanovic S, Rice DW and Palmer JD (2004). Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?. BMC Evol Biol 4: 35
Steinke D, Vences M, Salzburger W and Meyer A (2005). TaxI: a software tool for DNA barcoding using distance methods. Philos Trans Roy Soc Lond B Biol Sci 360: 1975–1980
Stocking C and Gifford E (1959). Incorporation of thymidine into chloroplasts of Spirogyra. Biochem Biophys Res Commun 1: 159–164
Stoebe B, Martin W and Kowallik K V (1998). Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes. Pl Molec Biol Rep 16: 243–255
Sugiura C, Kobayashi Y, Aoki S, Sugita C and Sugita M (2003). Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucl Acids Res 31: 5324–5331
Suguira M (1992). The chloroplast genome. Plant Mol Biol 19: 149–168
Swiatek M, Kuras R, Sokolenko A, Higgs D, Olive J, Cinque G, Muller B, Eichacker LA, Stern DB, Bassi R, Herrmann RG and Wollman FA (2001). The chloroplast gene ycf9 encodes a photosystem II (PSII) core subunit, psbZ, that participates in PSII supramolecular architecture. Pl Cell 13: 1347–1368
Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucl Acids Res 35: e14
Takahashi Y, Rahire M, Breyton C, Popot JL, Joliot P and Rochaix JD (1996). The chloroplast ycf7 (petL) open reading frame of Chlamydomonas reinhardtii encodes a small functionally important subunit of the cytochrome b6f complex. EMBO J 15: 3498–3506
Tang J, Xia H, Cao M, Zhang X, Zeng W, Hu S, Tong W, Wang J, Wang J, Yu J, Yang H and Zhu L (2004). A comparison of rice chloroplast genomes. Pl Physiol 135: 412–420
Taylor F (1987). An overview of the status of evolutionary cell symbiosis theories. Ann N Y Acad Sci 503: 1–16
Tillich M, Lehwark P, Morton BR and Maier U.G (2006). The evolution of chloroplast RNA editing. Molec Biol Evol 23: 1912–1921
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: 302–312
Timmis JN, Ayliffe MA, Huang CY and Martin W (2004). Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5: 123–135
Turmel M, Otis C and Lemieux C (1999). The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci USA 96: 10248–10253
Turmel M, Otis C and Lemieux C (2002). The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci USA 99: 11275–11280
Turmel M, Otis C and Lemieux C (2005). The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales. BMC Biol 3: 22
Peer Y and Wachter R (1997). Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Appl Biosci 13: 227–230
Wakasugi T, Nagai T, Kapoor M, Sugita M, Ito M, Ito S, Tsudzuki J, Nakashima K, Tsudzuki T, Suzuki Y, Hamada A, Ohta T, Inamura A, Yoshinaga K and Sugiura M (1997). Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc Natl Acad Sci USA 94: 5967–5972
Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T and Sugiura M (1994). Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 91: 9794–9798
Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, Ellis MW, Mishler BD, Kelch DG, Olmstead RG and Boore JL (2005). The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350: 117–128
Wolf PG, Rowe CA 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
Wolf PG, Rowe CA, Sinclair RB and Hasebe M (2003). Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res 10: 59–65
Wolfe KH, Morden CW and Palmer JD (1992). Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci USA 89: 10648–10652
Wyman S, Jansen R and Boore J (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252–3255
Xie Z and Merchant S (1996). The plastid-encoded ccsA gene is required for heme attachment to chloroplast c-type cytochromes. J Biol Chem 271: 4632–4639
Yoshinaga K, Iinuma H, Masuzawa T and Uedal K (1996). Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants. Nucl Acids Res 24: 1008–1014
Yoshinaga K, Kakehi T, Shima Y, Iinuma H, Masuzawa T and Ueno M (1997). Extensive RNA editing and possible double-stranded structures determining editing sites in the atpB transcripts of hornwort chloroplasts. Nucl Acids Res 25: 4830–4834
Yukawa M, Tsudzuki T and Sugiura M (2006). The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Molec Genet Genomics 275: 367–373
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Ravi, V., Khurana, J.P., Tyagi, A.K. et al. An update on chloroplast genomes. Plant Syst Evol 271, 101–122 (2008). https://doi.org/10.1007/s00606-007-0608-0
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DOI: https://doi.org/10.1007/s00606-007-0608-0