List of sequenced plastomes

A plastome is the genome of a plastid, a type of organelle found in plants and in a variety of protoctists. The number of known plastid genome sequences grew rapidly in the first decade of the twenty-first 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.

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 163,403 133 [15] Cycadaceae
Ephedra equisetina Ephedraceae
Ginkgo biloba 156,945 134 [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
Vaccinium macrocarpon 176,045 147 [68] Ericaceae
Vitis vinifera 160,928 [69] Vitaceae
Ximenia americana Ximeniaceae [58]
Yucca schidigera [16] Asparagaceae (sensu APG III)
Zea mays 140,384 110[19] [70] Poaceae

Green algae

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Bryopsis plumosa 106,859 115 [71]
Chaetosphaeridium globosum 131,183 124 [72]
Chara vulgaris
Chlamydomonas reinhardtii 203,395 99
Chlorella vulgaris 150,613 209 [73]
Chlorokybus atmophyticus 201,763 70 [74]
Dunaliella salina CCAP 19/18 269,044 102 [75]
Emiliania huxleyi 105,309 150
Helicosporidium 37,454 54 [76]
Leptosira terrestris 195,081 117 [77]
Mesostigma viride 42,424
Monomastix 114,528 94 [78]
Nephroselmis olivacea 200,799 127 [79]
Oedogonium cardiacum 196,547 103 [80]
Oltmannsiellopsis viridis 151,933 105 [81]
Ostreococcus tauri 71,666 86 [82]
Pseudendoclonium akinetum 195,867 105 [83]
Pycnococcus provasolii 80,211 98 [78]
Pyramimonas parkeae 101,605 110 [78]
Scenedesmus obliquus 161,452 96 [84]
Staurastrum punctulatum [85]
Stigeoclonium helveticum 223,902 97 [86]
Tydemania expeditionis 105,200 125 [71]
Ulva sp. UNA00071828 99,983 102 [87]
Volvox carteri 420,650 91 [88]
Zygnema circumcarinatum

Red algae

Sequenced Plastomes
Species variety Base Pairs Genes Reference Notes
Cyanidioschyzon merolae 149,987 243 [89]
Cyanidium caldarium RK1 [90]
Gracilaria tenuistipitata var. liui 183,883 238 [91]
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 [92]
Heterosigma akashiwo
Odontella sinensis 119.7kb 175
Phaeodactylum tricornutum
Thalassiosira pseudonana 129kb [93]
Rhodomonas salina

Chlorarachniophytes

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Bigelowiella natans 69,166 87 [94]

Euglenophytes

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Astasia longa 73.2kb 84
Euglena gracilis 143.2kb 128 [95]

Apicomplexans

Sequenced Plastomes
Species variety Base Pairs Genes Reference
Eimeria tenella Penn State 34.8kb 65 [96]
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 Paulinella chromatophora possesses an organelle (the 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 [97]

See also

References

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  4. ↑ Masanori Kugita; Akira Kaneko, Yuhei Yamamoto, Yuko Takeya, Tohoru Matsumoto and Koichi Yoshinaga (1986). "The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants". Nucleic Acids Research. 31 (2): 572–4. doi:10.1093/nar/gkg155.
  5. ↑ K Ohyama, Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Chang Z, Aota S, Inokuchi H, Ozeki H (2003). "Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA". Nature. 322 (6079): 716–721. doi:10.1038/322572a0.
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