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List of sequenced plastomes

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List of sequenced plastomes

A plants and in a variety of protoctists. The number of known plastid genome sequences grew rapidly in the first decade of the 21st century. For example, 25 chloroplast genomes were sequenced for one molecular phylogenetic study.[1]

The flowering plants are especially well represented in complete chloroplast genomes. As of March, 2010, all of their orders are represented except Petrosaviales, Pandanales, Liliales, Commelinales, Picramniales, Huerteales, Escalloniales, Bruniales, and Paracryphiales.

Contents

  • Plants 1
    • Bryophytes s.l. 1.1
    • Ferns and Lycophytes 1.2
    • Gymnosperms 1.3
    • Flowering plants 1.4
  • Green Algae 2
  • Red Algae 3
  • Glaucophytes 4
  • Meta-algae and Apicomplexans 5
    • photosynthetic Chromalveolates 5.1
    • Chlorarachniophytes 5.2
    • Euglenophytes 5.3
    • Apicomplexans 5.4
  • Nucleomorph Genomes 6
  • Cyanelle Genomes 7
  • See also 8
  • References 9
  • External links 10

Plants

Bryophytes s.l.

Sequenced Plastomes
Species variety Base Pairs Genes Reference Notes
Aneura mirabilis 108,007 [2][3] parasitic liverwort; plastome contains many pseudogenes
Anthoceros formosae 161,162 122 [4] hornwort; extensive RNA editing of plastome
Marchantia polymorpha 121,024 [5] liverwort
Physcomitrella patens 122,890 118 [6] moss
Tortula ruralis ~125,500 moss

Ferns and Lycophytes

Sequenced Plastomes
Species variety Base Pairs Genes Reference Family Notes
Adiantum capillus-veneris 150,568 [7] Pteridaceae
Alsophila spinulosa 156,661 117 [8] Cyatheaceae
Angiopteris evecta 153,901 [9] Marattiaceae
Equisetum arvense 133,309 Equisetaceae
Huperzia lucidula 154,373 [10] Lycopodiaceae
Isoetes flaccida 145,303 Isoetaceae
Psilotum nudum 138,829 117 [11] Psilotaceae
Selaginella moellendorffii Selaginellaceae
Selaginella uncinata 138,829 [12] Selaginellaceae

Gymnosperms

Sequenced Plastomes
Species variety Base Pairs Genes Reference Family Notes
Cryptomeria japonica 131,810 114 [13] Cupressaceae
Cycas micronesica [14] Cycadaceae
Cycas taitungensis [15] Cycadaceae
Ephedra equisetina Ephedraceae
Gingko biloba [16] Ginkgoaceae
Gnetum parvifolium Gnetaceae
Pinus koraiensis 116,866 Pinaceae
Pinus thunbergii 119,707 [17] Pinaceae
Podocarpus macrophyllus Podocarpaceae
Welwitschia mirabilis 119,726 101 [18] Welwitschiaceae

Flowering plants

Sequenced Plastomes
Species variety Base Pairs Genes Reference Family Notes
Acorus americanus [14] Acoraceae
Acorus calamus 153,821 Acoraceae
Aethionema cordifolium Brassicaceae
Aethionema grandiflorum Brassicaceae
Agrostis stolonifera 135,584 110 [19] Poaceae
Amborella trichopoda 162,686 [20] Amborellaceae
Anethum graveolens [14] Apiaceae
Antirrhinum majus [1] Plantaginaceae
Arabidopsis thaliana 154,478 [21] Brassicaceae
Arabis hirsuta Brassicaceae
Atropa belladonna 156,687 [22] Solanaceae
Aucuba japonica [1] Garryaceae
Bambusa oldhamii 139,350 Poaceae
Barbarea verna Brassicaceae
Berberidopsis corallina [1] Berberidopsidaceae
Brachypodium distachyon 135,199 110 [19] Poaceae
Brassica rapa Brassicaceae
Bulnesia arborea [1] Zygophyllaceae
Buxus microphylla [23] Buxaceae
Calycanthus floridus var. glaucus 153,337 [24] Calycanthaceae
Capsella bursa-pastoris Brassicaceae
Carica papaya Caricaceae
Ceratophyllum demersum [25] Ceratophyllaceae
Chloranthus spicatus [23] Chloranthaceae
Citrus sinensis var. 'Ridge Pineapple' 155,189 [26] Rutaceae
Coffea arabica [27] Rubiaceae
Coix lacryma-jobi [28] Poaceae
Cornus florida [1] Cornaceae
Crucihimalya wallichii Brassicaceae
Cucumis sativus 155,293 [29] Cucurbitaceae
Cuscuta exaltata [30] Convolvulaceae
Cuscuta gronovii [31] Convolvulaceae
Cuscuta obtusiflora Convolvulaceae
Cuscuta reflexa Convolvulaceae
Daucus carota 155,911 [32] Apiaceae
Dendrocalamus latiflorus 139,365 Poaceae
Dillenia indica [1] Dilleniaceae
Dioscores elephantipes [23] Dioscoreaceae
Draba nemorosa Brassicaceae
Drimys granadensis 160,604 [33] Winteraceae
Ehretia acuminata [1] Boraginaceae
Elaeis oleifera [14] Arecaceae
Epifagus virginiana 70,028 42 [34] Orobanchaceae
Eucalyptus globulus subsp. globulus 160,286 [35] Myrtaceae
Euonymus americanus [1] Celastraceae
Fagopyrum esculentum ssp. ancestrale 159,599 [36] Polygonaceae
Festuca arundinacea Poaceae
Ficus sp. [1] Moraceae
Glycine max 152,218 [37] Fabaceae
Gossypium barbadense 160,317 114 [38] Malvaceae
Gossypium hirsutum 160,301 [39] Malvaceae
Guizotia abyssinica Asteraceae
Gunnera manicata [1] Gunneraceae
Hedyosmum unpublished Chloranthaceae
Helianthus annuus 151,104 [40] Asteraceae
Heuchera sanguinea [1] Saxifragaceae
Hordeum vulgare subsp. vulgare 136,482 110 [19] Poaceae
Trithuria (syn. Hydatella) unpublished Hydatellaceae
Ilex cornuta [1] Aquifoliaceae
Illicium oligandrum [23] Schisandraceae (sensu APG III)
Ipomoea purpurea [30] Convolvulaceae
Jasminum nudiflorum 165,121 [41] Oleaceae
Lactuca sativa 152,765 [40] Asteraceae
Lemna minor 165,955 [42] Araliaceae
Lepidium virginicum Brassicaceae
Liquidambar styraciflua (syn. Altingia styraciflua) [1] Altingiaceae
Liriodendron tulipifera 159,866 [33][43] Magnoliaceae
Lobularia maritima Brassicaceae
Lolium perenne 135,282 110 [19] Poaceae
Lonicera japonica [1] Caprifoliaceae
Lotus corniculatus Fabaceae
Lotus japonicus 150,519 [44] Fabaceae
Manihot esculenta [45] Euphorbiaceae
Medicago truncatulata 124,033 Fabaceae
Megaleranthis saniculifolia 159,924 Ranunculaceae
Meliosma cuneifolia [1] Sabiaceae
Morus indica 156,599 [46] Moraceae
Musa acuminata [14] Musaceae
Nandina domestica [47] Berberidaceae
Nasturtium officinale Brassicaceae
Nelumbo nucifera [1] Nelumbonaceae
Nerium oleander Apocynaceae
Nicotiana sylvestris 155,941 Solanaceae
Nicotiana tabacum 155,943 [48] Solanaceae
Nicotiana tomentosiformis 155,745 Solanaceae
Nuphar advena 160,866 117 [49] Nymphaeaceae
Nymphaea alba 159,930 [50] Nymphaeaceae
Oenothera argillicola strain douthat 1 165,055 113 [51] Onagraceae
Oenothera biennis strain suaveolens Grado 164,807 113 [51] Onagraceae
Oenothera elata subsp. hookeri strain johansen 165,728 113 [51] Onagraceae
Oenothera glazioviana strain rr-lamarckiana Sweden 165,225 113 [51] Onagraceae
Oenothera parviflora strain atrovirens Standard 163,365 113 [51] Onagraceae
Olimarabidopsis pumila Brassicaceae
Oryza nivara 134,494 Poaceae
Oryza sativa indica 93-11 134,496 [52] Poaceae
Oryza sativa japonica Nipponbare 134,551 110[19] [53] Poaceae
Oryza sativa japonica PA64S 134,551 [52] Poaceae
Oxalis latifolia [1] Oxalidaceae
Panax ginseng 156,318 [54] Araliaceae
Passiflora biflora [14] Passifloraceae
Pelargonium × hortorum [55] Geraniaceae
Phalaenopsis aphrodite subsp. formosana 148,964 [56] Orchidaceae
Phaseolus vulgaris 'Negro Jamapa' 150,285 [57] Fabaceae
Phoenix dactylifera Arecaceae
Phoradendron leucarpum [1] Viscaceae [58]
Piper cenocladum 160,624 [33] Piperaceae
Platanus occidentalis 161,791 [47] Platanaceae
Plumbago auriculata [1] Plumbaginaceae
Populus alba 156,505 [59] Salicaceae
Populus trichocarpa [60] Salicaceae
Quercus nigra [1] Fagaceae
Ranunculus macranthus 155,158 117 [49] Ranunculaceae
Rhizanthella gardneri 59,190 33 [61] Orchidaceae subterranean mycoheterotroph
Rhododendron simsii [1] Ericaceae
Saccharum SP-80-3280 141,182 Poaceae
Saccharum officinarum 141,182 110 [19] Poaceae
Scaevola aemula [14] Goodeniaceae
Solanum bulbocastanum 155,371 Solanaceae
Solanum lycopersicum 155,460 Solanaceae
Solanum tuberosum 155,298 [62] Solanaceae
Staphylea colchica [1] Staphyleaceae
Sorghum bicolor 140,754 110 [19] Poaceae
Spinacia oleracea 150,725 [63] Amaranthaceae
Trachelium caeruleum [64] Campanulaceae
Trifolium subterraneum 144,763 111 [65] Fabaceae
Triticum aestivum cv. Chinese Spring 134,545 110[19] [66][67] Poaceae
Trochodendron aralioides [1] Trochodendraceae
Typha latifolia 165,572 113 [19] Typhaceae
Vitis vinifera 160,928 [68] Vitaceae
Ximenia americana Ximeniaceae [58]
Yucca schidigera [16] Asparagaceae (sensu APG III)
Zea mays 140,384 110[19] [69] Poaceae

Green Algae

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Chaetosphaeridium globosum 131,183 124 [70]
Chara vulgaris
Chlamydomonas reinhardtii 203,395 99
Chlorella vulgaris 150,613 209 [71]
Chlorokybus atmophyticus 201,763 70 [72]
Dunaliella salina CCAP 19/18 269,044 102 [73]
Emiliania huxleyi 105,309 150
Helicosporidium 37,454 54 [74]
Leptosira terrestris 195,081 117 [75]
Mesostigma viride 42,424
Monomastix 114,528 94 [76]
Nephroselmis olivacea 200,799 127 [77]
Oedogonium cardiacum 196,547 103 [78]
Oltmannsiellopsis viridis 151,933 105 [79]
Ostreococcus tauri 71,666 86 [80]
Pseudendoclonium akinetum 195,867 105 [81]
Pycnococcus provasolii 80,211 98 [76]
Pyramimonas parkeae 101,605 110 [76]
Scenedesmus obliquus 161,452 96 [82]
Staurastrum punctulatum [83]
Stigeoclonium helveticum 223,902 97 [84]
Volvox carteri 420,650 91 [85]
Zygnema circumcarinatum

Red Algae

Sequenced Plastomes
Species variety Base Pairs Genes Reference Notes
Cyanidioschyzon merolae 149,987 243 [86]
Cyanidium caldarium RK1 [87]
Gracilaria tenuistipitata var. liui 183,883 238 [88]
Porphyra purpurea
Porphyra yezoensis

Glaucophytes

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Cyanophora paradoxa

Meta-algae and Apicomplexans

Meta-algae are organisms with photosynthetic organelles of secondary or tertiary endosymbiotic origin, and their close non-photosynthetic, plastid-bearing, relatives. Apicomplexans are a secondarily non-photosynthetic group of chromalveoates which retain a reduced plastid organelle.

photosynthetic Chromalveolates

Dinoflagellate plastid genomes are not organised into a single circular DNA molecule like other plastid genomes, but into an array of mini-circles.

Sequenced Plastomes
Species variety Base Pairs Genes Reference Notes
Chromera velia
Guillardia theta 121,524 167 [89]
Heterosigma akashiwo
Odontella sinensis 119.7kb 175
Phaeodactylum tricornutum
Thalassiosira pseudonana 129kb [90]
Rhodomonas salina

Chlorarachniophytes

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Bigelowiella natans 69,166 87 [91]

Euglenophytes

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Astasia longa 73.2kb 84
Euglena gracilis 143.2kb 128 [92]

Apicomplexans

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Eimeria tenella Penn State 34.8kb 65 [93]
Plasmodium falciparum 34.7kb 68
Theileria parva Mugaga 39.6kb 71
Toxoplasma gondii RH 35.0kb 65

Nucleomorph Genomes

In some photosynthetic organisms that ability was acquired via symbiosis with a unicellular green alga (chlorophyte) or red alga (rhodophyte). In some such cases not only does the chloroplast of the former unicellular alga retain its own genome, but a remnant of the alga is also retained. When this retains a nucleus and a nuclear genome it is termed a nucleomorph.

Sequenced Nucleomorph Genomes
Species variety Base Pairs Genes Reference
Bigelowiella natans
Cryptomonas paramecium
Guillardia theta 551,264
Hemiselmis andersenii

Cyanelle Genomes

The unicellular eukaryote cyanelle) which represents an independent case of the acquisition of photosynthesis by cyanobacterial endosymbiosis. (Note: the term cyanelle is also applied to the plastids of glaucophytes.)

Sequenced Cyanelle Genomes
Species variety Base Pairs Genes Reference
Paulinella chromatophora 1.02Mb 867 [94]

See also

References

  1. ^ a b c d e f g h i j k l m n o p q r s t u v w x Moore, M. J.; Soltis, P. S.; Bell, C. D.; Burleigh, J. G.; Soltis, D. E. (2010). "Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots". Proceedings of the National Academy of Sciences of the United States of America 107 (10): 4623–4628.  
  2. ^ Wickett NJ, Zhang Y, Hansen SK et al. (February 2008). "Aneura mirabilis"Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort . Mol. Biol. Evol. 25 (2): 393–401.  
  3. ^ Plastid genome evolution of the non-photosynthetic liverwort Aneura mirabilis (Malmb.) Wickett & Goffinet (Aneuraceae)
  4. ^ Masanori Kugita; Akira Kaneko, Yuhei Yamamoto, Yuko Takeya, Tohoru Matsumoto and Koichi Yoshinaga (1986). ) chloroplast genome: insight into the earliest land plants"Anthoceros formosae"The complete nucleotide sequence of the hornwort (. Nucleic Acids Research 31 (2): 572–4.  
  5. ^ K Ohyama, Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Chang, Zhen, Aota, Shin-Ichi, Inokuchi, Hachiro, Ozeki, Haruo (2003). "Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA". Nature 322 (6079): 716–721.  
  6. ^ Chika Sugiura; Yuki Kobayashi, Setsuyuki Aoki1, Chieko Sugita and Mamoru Sugita (2003). "Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus". Nucleic Acids Research 31 (18): 5324–5331.  
  7. ^ Wolf, P. G.; Rowe, CA; Sinclair, RB; Hasebe, M (2003). "Complete Nucleotide Sequence of the Chloroplast Genome from a Leptosporangiate Fern, Adiantum capillus-veneris L". DNA Research 10 (2): 59–65.  
  8. ^ Lei Gao, Xuan Yi, Yong-Xia Yang, Ying-Juan Su, and Ting Wang. 2009. "Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes". BMC Evolutionary Biology 9:130 (11 Jun 2009). doi:10.1186/1471-2148-9-130
  9. ^ Roper, Jessie M.; Kellon Hansen, S.; Wolf, Paul G.; Karol, Kenneth G.; Mandoli, Dina F.; Everett, Karin D. E.; Kuehl, Jennifer; Boore, Jeffrey L. (2007). "The Complete Plastid Genome Sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae)". American Fern Journal 97 (2): 95–106.  
  10. ^ Wolf, Paul G.; Karol, Kenneth G.; Mandoli, Dina F.; Kuehl, Jennifer; Arumuganathan, K.; Ellis, Mark W.; Mishler, Brent D.; Kelch, Dean G. et al. (2005). "The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)". Gene 350 (2): 117–128.  
  11. ^ Tatsuya Wakasugi, A. Nishikawa, Kyoji Yamada, and Masahiro Sugiura. 1998. "Complete nucleotide sequence of the plastid genome from a fern, Psilotum nudum". Endocytobiology and Cell Research 13(supplement):147. see External links below.
  12. ^ Tsuji, Sumika; Ueda, Kunihiko; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Yoshikawa, Sumi; Konagaya, Akihiko; Nishiuchi, Takumi; Yamaguchi, Kazuo (2007). "The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses". Journal of Plant Research 120 (2): 281–290.  
  13. ^ Hirao T, Watanabe A, Kurita M, Kondo T, Takata K (2008). "Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species". BMC Plant Biol. 8: 70.  
  14. ^ a b c d e f g Jansen, R. K.; Cai, Z.; Raubeson, L. A.; Daniell, H.; Depamphilis, C. W.; Leebens-Mack, J.; Muller, K. F.; Guisinger-Bellian, M. et al. (2007). "Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns". Proceedings of the National Academy of Sciences 104 (49): 19369–19374.  
  15. ^ CS Wu; Wang YN; Liu SM; Chaw SM (2007). "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". Mol Biol Evol 24 (6): 1366–1379.  
  16. ^ a b J Leebens-Mack; Raubeson LA; Cui L; Kuehl J; Fourcade M; Chumley T; Boore JL; Jansen RK; dePamphilis CW (2005). "Identifying the basal angiosperms in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone". Mol Biol Evol 22 (10): 1948–1963.  
  17. ^ T Wakasugi; Tsudzuki J; Ito S; Nakashima K; Tsudzuki T; Sugiura M (1998). "Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii". PNAS 91 (21): 9794–9798.  
  18. ^ Skip R McCoy; Jennifer V Kuehl, Jeffrey L Boore and Linda A Raubeson (2008). "The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates". BMC Evolutionary Biology 8: 130.  
  19. ^ a b c d e f g h i j Guisinger et al, Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae, J Mol Evol 70: 149–166 (2010)
  20. ^ W Goremykin; Hirsch-Ernst KI; Wolfl S; Hellwig FH (2003). "Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm". Mol Bio Evol 20: 1445–1454. 
  21. ^ Sato, S.; Nakamura, Y; Kaneko, T; Asamizu, E; Tabata, S (1999). "Complete Structure of the Chloroplast Genome of Arabidopsis thaliana". DNA Research 6 (5): 283–290.  
  22. ^ Schmitz-Linneweber, C; Regel, R; Du, TG; Hupfer, H; Herrmann, RG; 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 Plant Speciation". Molecular Biology and Evolution 19 (9): 1602–1612.  
  23. ^ a b c d DR Hansen; Dastidar SG; Cai Z; Penaflor C; Kuehl JV; Boore JL; Jansen RK (2008). "Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)". Molecular Phylogenetics and Evolution 45 (2): 547–563.  
  24. ^ Goremykin, V.; Hirsch-Ernst, K. I.; w�Lfl, S.; Hellwig, F. H. (2003). "The chloroplast genome of the basal angiosperm Calycanthus fertilis – structural and phylogenetic analyses". Plant Systematics and Evolution 242 (1–4): 119–135.  
  25. ^ Michael J. Moore; Charles D. Bell; Pamela S. Soltis; Douglas E. Soltis (2007). "Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms". PNAS 104 (49): 19363–19368.  
  26. ^ Bausher, Michael G; Singh, Nameirakpam D; Lee, Seung-Bum; Jansen, Robert K; Daniell, Henry (2006). "The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms". BMC Plant Biology 6: 21.  
  27. ^ Samson, Nalapalli; Bausher, Michael G.; Lee, Seung-Bum; Jansen, Robert K.; Daniell, Henry (2007). "The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms". Plant Biotechnology Journal 5 (2): 339–353.  
  28. ^ Leseberg, Charles H.; Duvall, Melvin R. (2009). "The Complete Chloroplast Genome of Coix lacryma-jobi and a Comparative Molecular Evolutionary Analysis of Plastomes in Cereals". Journal of Molecular Evolution 69 (4): 311–318.  
  29. ^ Pląder, Wojciech; Yukawa, Yasushi; Sugiura, Masahiro; Malepszy, Stefan (2007). "The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis". Cellular and Molecular Biology Letters 12 (4): 584–594.  
  30. ^ a b McNeal, Joel R; Kuehl, Jennifer V; Boore, Jeffrey L; De Pamphilis, Claude W (2007). "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta". BMC Plant Biology 7: 57.  
  31. ^ Funk HT, Berg S, Krupinska K, Maier UG, Krause K (2007). "Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii". BMC Plant Biol. 7: 45.  
  32. ^ Ruhlman, Tracey; Lee, Seung-Bum; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry (2006). "Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms". BMC Genomics' 7: 222.  
  33. ^ a b c Cai, Zhengqiu; Penaflor, Cynthia; Kuehl, Jennifer V; Leebens-Mack, James; Carlson, John E; Depamphilis, Claude W; Boore, Jeffrey L; Jansen, Robert K (2006). "Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids". BMC Evolutionary Biology 6: 77.  
  34. ^ Wolfe KH, Morden CW, Palmer JD (November 1992). "Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant". Proc. Natl. Acad. Sci. U.S.A. 89 (22): 10648–52.  
  35. ^ Steane, D. A. (2005). "Complete Nucleotide Sequence of the Chloroplast Genome from the Tasmanian Blue Gum, Eucalyptus globulus (Myrtaceae)". DNA Research 12 (3): 215–220.  
  36. ^ Maria D Logacheva; Tahir H Samigullin, Amit Dhingra and Aleksey A Penin (2008). "Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale – A wild ancestor of cultivated buckwheat". BMC Plant Biology 8: 59.  
  37. ^ Saski, Christopher; Lee, Seung-Bum; Daniell, Henry; Wood, Todd C.; Tomkins, Jeffrey; Kim, Hyi-Gyung; Jansen, Robert K. (2005). "Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes". Plant Molecular Biology 59 (2): 309–322.  
  38. ^ Rashid Ismael Hag Ibrahim; Jun-Ichi Azuma and Masahiro Sakamoto (2006). L.) Chloroplast Genome with a Comparative Analysis of Sequences among 9 Dicot Plants"Gossypium barbadense"Complete Nucleotide Sequence of the Cotton (. Genes & Genetic Systems 81 (5): 311–321.  
  39. ^ Lee, Seung-Bum; Kaittanis, Charalambos; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry (2006). "The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms". BMC Genomics 7: 61.  
  40. ^ a b 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". American Journal of Botany 94 (3): 302–312.  
  41. ^ Lee, H.-L.; Jansen, R. K.; Chumley, T. W.; Kim, K.-J. (2007). "Gene Relocations within Chloroplast Genomes of Jasminum and Menodora (Oleaceae) Are Due to Multiple, Overlapping Inversions". Molecular Biology and Evolution 24 (5): 1161–1180.  
  42. ^ Mardanov, Andrey V.; Ravin, Nikolai V.; Kuznetsov, Boris B.; Samigullin, Tahir H.; Antonov, Andrey S.; Kolganova, Tatiana V.; Skyabin, Konstantin G. (2008). "Complete Sequence of the Duckweed (Lemna minor) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to Other Angiosperms". Journal of Molecular Evolution 66 (6): 555–564.  
  43. ^ Haiying Liang, John E. Carlson, James H. Leebens-Mack, P. Kerr Wall, Lukas A. Mueller, Matyas Buzgo< Lena L. Landherr, Yi Hu, D. Scott DiLoreto, Daniel C. Ilut, Dawn Field, Steven D. Tanksley, Hong Ma, and Claude W. dePamphilis. 2008. "An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron". Tree Genetics and Genomes 4(3):419-433. doi:10.1007/s11295-007-0120-2
  44. ^ Kato, T; Kaneko, T; Sato, S; Nakamura, Y; Tabata, S (2000). "Complete Structure of the Chloroplast Genome of a Legume, Lotus japonicus". DNA Research 7 (6): 323–330.  
  45. ^ Daniell, Henry; Wurdack, Kenneth J.; Kanagaraj, Anderson; Lee, Seung-Bum; Saski, Christopher; Jansen, Robert K. (2008). ) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron"Manihot esculenta"The complete nucleotide sequence of the cassava (. Theoretical and Applied Genetics 116 (5): 723–737.  
  46. ^ Ravi, V.; Khurana, Jitendra P.; Tyagi, Akhilesh K.; Khurana, Paramjit (2006). "The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis". Tree Genetics and Genomes 3 (1): 49–59.  
  47. ^ a b Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E (2006). "Rapid and accurate pyrosequencing of angiosperm plastid genomes". BMC Plant Biology 6: 17.  
  48. ^ 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, B. Y.; Sugita, M; Deno, H; Kamogashira, T; Yamada, K; Kusuda, J; Takaiwa, F; Kato, A; Tohdoh, N; Shimada, H; Sugiura, M (1986). "The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression". The EMBO Journal 5 (9): 2043–2049.  
  49. ^ a b Linda A Raubeson; Rhiannon Peery, Timothy W Chumley, Chris Dziubek, H Matthew Fourcade, Jeffrey L Boore and Robert K Jansen (2007). "Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus". BMC Genomics 8: 174.  
  50. ^ Goremykin, V. V.; Hirsch-Ernst, KI; Wölfl, S; Hellwig, FH (2004). "The Chloroplast Genome of Nymphaea alba: Whole-Genome analyses and the Problem of Identifying the Most Basal Angiosperm". Molecular Biology and Evolution 21 (7): 1445–1454.  
  51. ^ a b c d e Stephan Greiner; Xi Wang, Uwe Rauwolf, Martina V. Silber, Klaus Mayer, Jörg Meurer, Georg Haberer and Reinhold G. Herrmann (2008). "The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution". Nucleic Acids Research 36 (7): 2366–78.  
  52. ^ a b Jun Yu et alii (117 authors). 2005. "The Genomes of Oryza sativa: a history of duplications". PLoS Biology 3(2):e38. Epub 2005 Feb 1.
  53. ^ Hiratsuka, J; Shimada, H; Whittier, R; Ishibashi, T; Sakamoto, M; Mori, M; Kondo, C; Honji, 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". Molecular and General Genetics 217 (2–3): 185–194.  
  54. ^ Kim, K.-J.; Lee, HL (2004). "Complete Chloroplast Genome Sequences from Korean Ginseng (Panax schinseng Nees) and Comparative Analysis of Sequence Evolution among 17 Vascular Plants". DNA Research 11 (4): 247–261.  
  55. ^ Chumley, TW; Palmer, JD; Mower, JP; Fourcade, HM; Calie, PJ; Boore, JL; Jansen, RK (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". Molecular Biology and Evolution 23 (11): 2175–2190.  
  56. ^ Chang, C.-C.; Lin, HC; Lin, IP; Chow, TY; Chen, HH; Chen, WH; Cheng, CH; Lin, CY et al. (2006). "The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with that of Grasses and Its Phylogenetic Implications". Molecular Biology and Evolution 23 (2): 279–291.  
  57. ^ Xianwu Guo; Santiago Castillo-Ramírez; Víctor González; 1 Patricia Bustos; José Luís Fernández-Vázquez; Rosa Isela Santamaría; 1 Jesús Arellano; 2 Miguel A Cevallos; Guillermo Dávila (2007). "Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts". BMC Genonomics 8: 288.  
  58. ^ a b "A revised classification of Santalales". Taxon 59 (2): 538–558. 2010. 
  59. ^ Okumura, Satoru; Sawada, Machiko; Park, Yong Woo; Hayashi, Takahisa; Shimamura, Masaki; Takase, Hisabumi; Tomizawa, Ken-Ichi (2006). "Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts". Transgenic Research 15 (5): 637–646.  
  60. ^ Gerald A. Tuskan, et alii (110 authors). 2006. "The genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)". Science 313 (5793):1596-1604.
  61. ^ Etienne Delannoy, Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes, Molecular Biology and Evolution advance access (Feb 2011)
  62. ^ Chung, Hwa-Jee; Jung, Jong Duk; Park, Hyun-Woo; Kim, Joo-Hwan; Cha, Hyun Wook; Min, Sung Ran; Jeong, Won-Joong; Liu, Jang Ryol (2006). "The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence". Plant Cell Reports 25 (12): 1369–1379.  
  63. ^ Schmitz-Linneweber, C; Maier, RM; Alcaraz, JP; Cottet, A; Herrmann, RG; Mache, R (2001). "The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization". Plant Molecular Biology 45 (3): 307–315.  
  64. ^ Rosemarie C. Haberle, H. Matthew Fourcade, Jeffrey L. Boore, and Robert K. Jansen. 2008. "Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes". Journal of Molecular Evolution 66(4):350=361. doi:10.1007/s00239-008-9086-4
  65. ^ Zhengqiu Cai et al, Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions, J Mol Evol 67: 696–704 (2008)doi:10.1007/s00239-008-9180-7
  66. ^ Ogihara, Yasunari; Isono, Kazuriho; Kojima, Toshio; Endo, Akira; Hanaoka, Mitsumasa; Shiina, Takashi; Terachi, Toru; Utsugi, Shigeko et al. (2000). "Chinese Spring Wheat (Triticum aestivum L.) Chloroplast Genome: Complete Sequence and Contig Clones". Plant Molecular Biology Reporter 18 (3): 243–253.  
  67. ^ y., Ogihara; k., Isono; t., Kojima; a., Endo; m., Hanaoka; t., Shiina; t., Terachi; s., Utsugi et al. (2002). "Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA". Molecular Genetics and Genomics 266 (5): 740–746.  
  68. ^ Jansen, Robert K; Kaittanis, Charalambos; Saski, Christopher; Lee, Seung-Bum; Tomkins, Jeffrey; Alverson, Andrew J; Daniell, Henry (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 Evolutionary Biology 6: 32.  
  69. ^ Maier, RM; Neckermann, K; Igloi, GL; Kössel, H (1995). "Complete Sequence of the Maize Chloroplast Genome: Gene Content, Hotspots of Divergence and Fine Tuning of Genetic Information by Transcript Editing". Journal of Molecular Biology 251 (5): 614–628.  
  70. ^ Turmel M, Otis C, Lemieux C (August 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. U.S.A. 99 (17): 11275–80.  
  71. ^ Wakasugi T, Nagai T, Kapoor M et al. (May 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. U.S.A. 94 (11): 5967–72.  
  72. ^ Turmel M, Otis C, Lemieux C (2007). "An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus". BMC Genomics 8: 137.  
  73. ^ Smith et al.; Lee, RW; Cushman, JC; Magnuson, JK; Tran, D; Polle, JE (2010). organelle genomes: large sequences, inflated with intronic and intergenic DNA"Dunaliella salina"The .  
  74. ^ de Koning AP, Keeling PJ (2006). "The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured". BMC Biol. 4: 12.  
  75. ^ de Cambiaire JC, Otis C, Turmel M, Lemieux C (2007). "The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae". BMC Genomics 8: 213.  
  76. ^ a b c Monique Turmel, Marie-Christine Gagnon*, Charley J. O'Kelly, Christian Otis* and Claude Lemieux (March 2009). "The Chloroplast Genomes of the Green Algae Pyramimonas, Monomastix, and Pycnococcus Shed New light on the Evolutionary History of Prasinophytes and the Origin of the Secondary Chloroplasts of Euglenids". Molecular Biology and Evolution 26 (3): 631–648.  
  77. ^ Turmel M, Otis C, Lemieux C (August 1999). "The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes". Proc. Natl. Acad. Sci. U.S.A. 96 (18): 10248–53.  
  78. ^ Brouard JS, Otis C, Lemieux C, Turmel M (2008). "Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer". BMC Genomics 9: 290.  
  79. ^ Pombert JF, Lemieux C, Turmel M (2006). "The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes". BMC Biol. 4: 3.  
  80. ^ Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y (April 2007). "The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction". Mol. Biol. Evol. 24 (4): 956–68.  
  81. ^ Pombert JF, Otis C, Lemieux C, Turmel M (September 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". Mol. Biol. Evol. 22 (9): 1903–18.  
  82. ^ de Cambiaire JC, Otis C, Lemieux C, Turmel M (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.  
  83. ^ Turmel M, Otis C, 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.  
  84. ^ Bélanger AS, Brouard JS, Charlebois P, Otis C, Lemieux C, Turmel M (November 2006). "Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum". Mol. Genet. Genomics 276 (5): 464–77.  
  85. ^ Smith, David Roy and Lee, Robeert W (March 2009). "The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA". BMC Genomics 10 (132): 132.  
  86. ^ Niji Ohta; Motomichi Matsuzaki, Osami Misumi, Shin-ya Miyagishima, Hisayoshi Nozaki, Kan Tanaka, Tadasu Shin-I, Yuji Kohara and Tsuneyoshi Kuroiwa (2003). "Cyanidioschyzon merolae"Complete Sequence and Analysis of the Plastid Genome of the Unicellular Red Alga . DNA Research 10 (2): 67–77.  
  87. ^ Gernot Glöckner; André Rosenthal and Klaus Valentin (2000). "The Structure and Gene Repertoire of an Ancient Red Algal Plastid Genome". Journal of Molecular Evolution 51 (4): 382–90.  
  88. ^ JC Hagopian; Reis M; Kitajima JP; Bhattacharya D; de 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". Journal of Molecular Evolution 59 (4): 464–77.  
  89. ^ Susan E. Douglas; Susanne L. Penny (1999). : Complete Sequence and Conserved Synteny Groups Confirm Its Common Ancestry with Red Algae"Guillardia theta"The Plastid Genome of the Cryptophyte Alga, . Journal of Molecular Evolution 48 (2): 236–44.  
  90. ^ E. Virginia Armbrust, et alii (42 authors). 2004. "The Genome of the Diatom Thalassiosira pseudonana: Ecology, Evolution, and Metabolism". Science 306(5693):79-86.
  91. ^ Matthew B. Rogers; Paul R. Gilson, Vanessa Su, Geoffrey I. McFadden,� and Patrick J. Keeling (2007). "The Complete Chloroplast Genome of the Chlorarachniophyte Bigelowiella natans: Evidence for Independent Origins of Chlorarachniophyte and Euglenid Secondary Endosymbionts". Mol. Biol. Evol 24 (1): 54–62.  
  92. ^ Hallick RB; Hong L; Drager RG; Favreau MR; Monfort A; Orsat B; Spielmann A; Stutz E. (1993). "Complete sequence of Euglena gracilis chloroplast DNA". Nucleic Acids Research 21 (15): 3537–44.  
  93. ^ X Cai; Fuller AL; McDougald LR; Zhu G (2003). "Apicoplast genome of the coccidian Eimeria tenella". Gene 321: 39–46.  
  94. ^ Eva C.M. Nowack;  

External links

  • HAMAP proteomes: Plastids
  • Complete Plastid Genomes
  • Chloroplast Genome Database
  • NCBI Eukaryotic Plastid Genomes
  • chloroplast genome list In: Montreal genomics
  • Psilotum nudum
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