Biology:List of sequenced plastomes

From HandWiki
List of plastid genomes whose DNA sequence is known
The 156 kb plastome gene map of Nicotiana tabacum.
The 154 kb plastid genome map of a model flowering plant (Arabidopsis thaliana: Brassicaceae).
The highly reduced, 27 kb plastome map of the parasitic Hydnora visseri.

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 January, 2017, all of their orders are represented except Commelinales, Picramniales, Huerteales, Escalloniales, Bruniales, and Paracryphiales.

A compilation of all available complete plastid genomes is maintained by the NCBI in a public repository.[2]

Plants

Bryophytes s.l.

Sequenced Plastomes
Species Variety Size (bp) Genes Reference Notes
Aneura mirabilis 108,007 [3][4] parasitic liverwort; plastome contains many pseudogenes
Anthoceros formosae 161,162 122 [5] hornwort; extensive RNA editing of plastome
Marchantia polymorpha 121,024 [6] liverwort
Nothoceros aenigmaticus 153,208 124 [7] hornwort
Pellia endiviifolia 120,546 123 [8] liverwort
Physcomitrella patens 122,890 118 [9] moss
Ptilidium pulcherrimum 119,007 122 [10] liverwort
Tortula ruralis 122,630 [11] moss

Ferns and Lycophytes

Sequenced Plastomes
Species Variety Size (bp) Genes Reference Family Notes
Adiantum capillus-veneris 150,568 [12] Pteridaceae
Alsophila spinulosa 156,661 117 [13] Cyatheaceae
Angiopteris evecta 153,901 [14] Marattiaceae
Equisetum arvense 133,309 Equisetaceae
Huperzia lucidula 154,373 [15] Lycopodiaceae
Isoetes flaccida 145,303 Isoetaceae
Psilotum nudum 138,829 117 Psilotaceae
Selaginella uncinata 138,829 [16] Selaginellaceae
Sequenced fern and lycophyte plastomes without information about size, number of genes and / or references.
Species Variety Size (bp) Genes Reference Family Notes
Equisetum hyemale Equisetaceae
Lygodium japonicum Lygodiaceae
Marsilea crenata Marsileaceae
Ophioglossum californicum Ophioglossaceae
Selaginella moellendorffii Selaginellaceae

Gymnosperms

Sequenced Plastomes
Species Variety Size (bp) Genes Reference Family Notes
Cryptomeria japonica 131,810 114 [17] Cupressaceae
Cycas micronesica [18] Cycadaceae
Cycas taitungensis 163,403 133 [19] Cycadaceae
Ephedra equisetina Ephedraceae
Ginkgo biloba 156,945 134 [20] Ginkgoaceae
Gnetum parvifolium Gnetaceae
Picea engelmannii Se404-851 123,542 114 [21] Pinaceae
Picea glauca PG29 123,266 114 [22] Pinaceae
Picea glauca WS77111 123,421 114 [23] Pinaceae
Picea sitchensis Q903 124,049 114 [24] Pinaceae
Pinus koraiensis 116,866 Pinaceae
Pinus thunbergii 119,707 [25] Pinaceae
Podocarpus macrophyllus Podocarpaceae
Welwitschia mirabilis 119,726 101 [26] Welwitschiaceae

Flowering plants

This sortable table is expected to compile complete plastid genomes representing the largest range of sizes, number of genes, and angiosperm families.

Sequenced plastomes with complete genome size, number of unique genes, reference and publication year.
Species Size (bp) Genes Reference Year Family Notes
Acorus americanus 153,819 [18] 2007 Acoraceae
Agrostis stolonifera 135,584 110 [27] 2010 Poaceae
Alniphyllum eberhardtii 155,384 113 [28] 2017 Styracaceae
Alstroemeria aurea 155,510 112 [29] 2013 Alstroemeriaceae
Amborella trichopoda 162,686 [30] 2003 Amborellaceae
Anethum graveolens 153,356 [18] 2007 Apiaceae
Arabidopsis thaliana 154,478 [31] 1999 Brassicaceae
Atropa belladonna 156,687 [32] 2002 Solanaceae
Brachypodium distachyon 135,199 110 [27] 2010 Poaceae
Buxus microphylla 159,010 113 [33] 2007 Buxaceae
Calycanthus floridus var. glaucus 153,337 115 [34] 2003 Calycanthaceae
Carpinus tientaiensis 160,104 114 [35] 2017 Betulaceae
Chloranthus spicatus 157,772 113 [33] 2007 Chloranthaceae
Citrus sinensis var. 'Ridge Pineapple' 155,189 [36] 2006 Rutaceae
Cocos nucifera 154,731 130 [37] 2013 Arecaceae
Coffea arabica 155,189 [38] 2007 Rubiaceae
Coix lacryma-jobi 140,745 [39] 2009 Poaceae
Conopholis americana 45,673 42 [40] 2013 Orobanchaceae Non-photosynthetic parasite
Cucumis sativus 155,293 [41] 2007 Cucurbitaceae
Cuscuta exaltata 125,373 [42] 2007 Convolvulaceae
Cuscuta gronovii 86,744 86 [43] 2007 Convolvulaceae
Cuscuta reflexa 121,521 98 [43] 2007 Convolvulaceae
Cypripedium formosanum 178,131 [44] 2015 Orchidaceae
Cytinus hypocistis 19,400 23 [45] 2016 Cytinaceae Holoparasitic
Daucus carota 155,911 [46] 2006 Apiaceae
Dioscores elephantipes 152,609 112 [33] 2007 Dioscoreaceae
Drimys granadensis 160,604 113 [47] 2006 Winteraceae
Epifagus virginiana 70,028 42 [48] 1992 Orobanchaceae
Epipogium aphyllum 30,650 27 [49] 2015 Orchidaceae Mycoheterotrophic
Epipogium roseum 19,047 29 [49] 2015 Orchidaceae Mycoheterotrophic
Erodium carvifolium 116,935 107 [50] 2016 Geraniaceae
Erodium chrysanthum 168,946 96 [50] 2016 Geraniaceae
Erodium texanum 130,812 106 [51] 2011 Geraniaceae
Eucalyptus globulus subsp. globulus 160,286 [52] 2005 Myrtaceae
Fagopyrum esculentum ssp. ancestrale 159,599 [53] 2008 Polygonaceae
Geranium palmatum 155,794 105 [51] 2011 Geraniaceae
Glycine max 152,218 [54] 2005 Fabaceae
Gossypium barbadense 160,317 114 [55] 2006 Malvaceae
Gossypium hirsutum 160,301 [56] 2006 Malvaceae
Helianthus annuus 151,104 [57] 2007 Asteraceae
Hordeum vulgare subsp. vulgare 136,482 110 [27] 2010 Poaceae
Hydnora visseri 27,233 24 [58] 2016 Aristolochiaceae Non-photosynthetic holoparasite
Illicium oligandrum 148,552 113 [33] 2007 Schisandraceae (sensu APG III)
Ipomoea purpurea 162,046 [42] 2007 Convolvulaceae
Jasminum nudiflorum 165,121 [59] 2007 Oleaceae
Juglans regia 160,367 129 [60] 2017 Juglandaceae
Lactuca sativa 152,765 [57] 2007 Asteraceae
Lemna minor 165,955 [61] 2008 Araliaceae
Licania alba 162,467 112 [62] 2014 Chrysobalanaceae
Lilium longiflorum 152,793 114 [29] 2013 Liliaceae
Liriodendron tulipifera 159,866 [47][63] 2006 Magnoliaceae
Lolium perenne 135,282 110 [27] 2010 Poaceae
Lonicera japonica 155,078 [1] 2010 Caprifoliaceae
Lotus japonicus 150,519 [64] 2000 Fabaceae
Manihot esculenta 161,453 [65] 2008 Euphorbiaceae
Monotropa hypopitys 35,336 45 [66] 2016 Ericaceae Mycoheterotrophic
Monsonia speciosa 128,787 106 [51] 2011 Geraniaceae
Morus indica 156,599 [67] 2006 Moraceae
Musa balbisiana 169,503 113 [68] 2016 Musaceae
Nandina domestica 156,599 [69] 2006 Berberidaceae
Neottia nidus-avis 92,060 56 [70] 2011 Orchidaceae Mycoheterotrophic
Nelumbo nucifera 163,330 [1] 2010 Nelumbonaceae
Nicotiana tabacum 155,943 113 [71] 1986 Solanaceae
Nuphar advena 160,866 117 [72] 2007 Nymphaeaceae
Nymphaea alba 159,930 [73] 2004 Nymphaeaceae
Oenothera argillicola strain Douthat 1 165,055 113 [74] 2008 Onagraceae
Oenothera biennis strain suaveolens Grado 164,807 113 [74] 2008 Onagraceae
Oenothera elata subsp. hookeri strain johansen Standard 165,728 113 [74] 2008 Onagraceae
Oenothera glazioviana strain r/r-lamarckiana Sweden 165,225 113 [74] 2008 Onagraceae
Oenothera parviflora strain atrovirens Standard 163,365 113 [74] 2008 Onagraceae
Oryza sativa indica 93-11 134,496 [75] 2005 Poaceae
Oryza sativa japonica Nipponbare 134,551 110 [76][27] 1989 Poaceae
Oryza sativa japonica PA64S 134,551 [75] 2005 Poaceae
Osyris alba 147,253 101 [77] 2015 Santalaceae Hemiparasitic
Panax ginseng 156,318 [78] 2004 Araliaceae
Pelargonium × hortorum 217,942 [79] 2006 Geraniaceae
Petrosavia stellaris 103,835 58 [80] 2014 Petrosaviaceae Mycoheterotrophic
Phalaenopsis aphrodite subsp. formosana 148,964 [81] 2006 Orchidaceae
Phaseolus vulgaris 'Negro Jamapa' 150,285 [82] 2007 Fabaceae
Pilostyles aethiopica 11,348 5 [83] 2016 Apodanthaceae Endo-holoparasite
Pilostyles hamiltonii 15,167 5 [83] 2016 Apodanthaceae Endo-holoparasite
Piper cenocladum 160,624 113 [47] 2006 Piperaceae
Platanus occidentalis 161,791 [69] 2006 Platanaceae
Populus alba 156,505 [84] 2006 Salicaceae
Ranunculus macranthus 155,158 117 [72] 2007 Ranunculaceae
Rhizanthella gardneri 59,190 33 [85] 2011 Orchidaceae Subterranean mycoheterotroph
Saccharum officinarum 141,182 110 [27] 2010 Poaceae
Sciaphila densiflora 21,485 28 [86] 2015 Triuridaceae Mycoheterotrophic
Solanum tuberosum 155,298 [87] 2006 Solanaceae
Sorghum bicolor 140,754 110 [27] 2010 Poaceae
Spinacia oleracea 150,725 [88] 2001 Amaranthaceae
Trachelium caeruleum 162,321 [89] 2008 Campanulaceae
Trifolium subterraneum 144,763 111 [90] 2008 Fabaceae
Triticum aestivum cv. Chinese Spring 134,545 110 [91][92][27] 2000 Poaceae
Typha latifolia 165,572 113 [27] 2010 Typhaceae
Vaccinium macrocarpon 176,045 147 [93] 2013 Ericaceae
Viscum album 128,921 96 [77] 2015 Viscaceae Hemiparasitic
Viscum minimum 131,016 99 [77] 2015 Viscaceae Hemiparasitic
Vitis vinifera 160,928 [94] 2006 Vitaceae
Yucca schidigera 156,158 [20] 2005 Asparagaceae (sensu APG III)
Zea mays 140,384 110 [95][27] 2010 Poaceae
Sequenced plastomes without information about size, number of genes and / or references.
Species Size (bp) Genes Reference Year Family Notes
Acorus calamus 153,821 Acoraceae
Aethionema cordifolium Brassicaceae
Aethionema grandiflorum Brassicaceae
Antirrhinum majus [1] 2010 Plantaginaceae
Arabis hirsuta Brassicaceae
Aucuba japonica [1] 2010 Garryaceae
Bambusa oldhamii 139,350 Poaceae
Barbarea verna Brassicaceae
Berberidopsis corallina [1] 2010 Berberidopsidaceae
Brassica rapa Brassicaceae
Bulnesia arborea [1] 2010 Zygophyllaceae
Capsella bursa-pastoris Brassicaceae
Carica papaya Caricaceae
Ceratophyllum demersum [96] 2007 Ceratophyllaceae
Cornus florida [1] 2010 Cornaceae
Crucihimalya wallichii Brassicaceae
Cuscuta obtusiflora Convolvulaceae
Cuscuta reflexa Convolvulaceae
Dendrocalamus latiflorus 139,365 Poaceae
Dillenia indica [1] 2010 Dilleniaceae
Draba nemorosa Brassicaceae
Ehretia acuminata [1] 2010 Boraginaceae
Elaeis oleifera [18] 2007 Arecaceae
Euonymus americanus [1] 2010 Celastraceae
Festuca arundinacea Poaceae
Ficus sp. [1] 2010 Moraceae
Guizotia abyssinica Asteraceae
Gunnera manicata [1] 2010 Gunneraceae
Hedyosmum unpublished Chloranthaceae
Heuchera sanguinea [1] 2010 Saxifragaceae
Ilex cornuta [1] 2010 Aquifoliaceae
Lepidium virginicum Brassicaceae
Liquidambar styraciflua (syn. Altingia styraciflua) [1] 2010 Altingiaceae
Lobularia maritima Brassicaceae
Lotus corniculatus Fabaceae
Medicago truncatulata 124,033 Fabaceae
Megaleranthis saniculifolia 159,924 Ranunculaceae
Meliosma cuneifolia [1] 2010 Sabiaceae
Nasturtium officinale Brassicaceae
Olimarabidopsis pumila Brassicaceae
Phoenix dactylifera Arecaceae
Nerium oleander 154,903 Apocynaceae
Nicotiana sylvestris 155,941 Solanaceae
Nicotiana tomentosiformis 155,745 Solanaceae
Oryza nivara 134,494 Poaceae
Oxalis latifolia [1] 2010 Oxalidaceae
Passiflora biflora [18] 2007 Passifloraceae
Phoradendron leucarpum [1] 2010 Viscaceae
Plumbago auriculata [1] 2010 Plumbaginaceae
Populus trichocarpa [97] 2006 Salicaceae
Quercus nigra [1] 2010 Fagaceae
Rhododendron simsii [1] 2010 Ericaceae
Scaevola aemula [18] 2007 Goodeniaceae
Solanum bulbocastanum 155,371 Solanaceae
Solanum lycopersicum 155,460 Solanaceae
Staphylea colchica [1] 2010 Staphyleaceae
Trithuria (syn. Hydatella) unpublished Hydatellaceae
Trochodendron aralioides [1] 2010 Trochodendraceae
Ximenia americana 2010 Ximeniaceae[98]

Green algae

Sequenced Plastomes
Species Variety Size (bp) Genes Reference
Bryopsis plumosa 106,859 115 [99]
Chaetosphaeridium globosum 131,183 124 [100]
Chara vulgaris
Chlamydomonas reinhardtii 203,395 99
Chlorella vulgaris 150,613 209 [101]
Chlorokybus atmophyticus 201,763 70 [102]
Dunaliella salina CCAP 19/18 269,044 102 [103]
Emiliania huxleyi 105,309 150
Helicosporidium 37,454 54 [104]
Leptosira terrestris 195,081 117 [105]
Mesostigma viride 42,424
Monomastix 114,528 94 [106]
Nephroselmis olivacea 200,799 127 [107]
Oedogonium cardiacum 196,547 103 [108]
Oltmannsiellopsis viridis 151,933 105 [109]
Ostreococcus tauri 71,666 86 [110]
Pseudendoclonium akinetum 195,867 105 [111]
Pycnococcus provasolii 80,211 98 [106]
Pyramimonas parkeae 101,605 110 [106]
Scenedesmus obliquus 161,452 96 [112]
Staurastrum punctulatum [113]
Stigeoclonium helveticum 223,902 97 [114]
Tydemania expeditionis 105,200 125 [99]
Ulva sp. UNA00071828 99,983 102 [115]
Volvox carteri 420,650 91 [116]
Zygnema circumcarinatum

Red algae

Sequenced Plastomes
Species Variety Size (bp) Genes Reference Year Taxon Notes
Ahnfeltia plicata 190,451 205 (coding) [117] 2016 Ahnfeltiales
Apophlaea sinclairii 182,437 189 (coding) [117] 2016 Hildenbrandiales
Asparagopsis taxiformis 177,091 203 (coding) [117] 2016
Bangiopsis subsimplex 204,784 194 (coding) [117] 2016
Calliarthron tuberculosum 178,981 238 [118] 2013
Ceramium japonicum 171,634 199 (coding) [117] 2016
Chondrus crispus 180,086 240 [118] 2013 Gigartinales
Cyanidioschyzon merolae 10D 149,987 243 [119] 2003
Cyanidium caldarium RK1 164,921 230 [120] 2000
Erythrotrichia carnea 210,691 191 (coding) [117] 2016
Galdieria sulphuraria 074W 167,741 233 [121] 2015
Gelidium elegans 174,748 234 [122] 2016
Gelidium sinicola UC276620 177,095 232 [123] 2019 May be synonymous with G. coulteri
Gelidium vagum 179,853 234 [122] 2016
Gracilaria changii 183,855 231 [124] 2018 Gracilariales
Gracilaria chorda 182,459 201 (coding) [117] 2016 Gracilariales
Gracilaria salicornia 179,757 235 [125] 2014 Gracilariales
Gracilaria tenuistipitata var. liui 183,883 238 [126] 2004 Gracilariales
Gracilaria vermiculophylla 180,254 239 unpublished Gracilariales
Grateloupia filicina 195,990 265 unpublished
Grateloupia taiwanensis 191,270 266 [127] 2013
Hildenbrandia rivularis 189,725 184 (coding) [117] 2016
Hildenbrandia rubra 180,141 190 (coding) [117] 2016
Kumanoa americana 184,025 234 [128] 2018
Palmaria palmata 192,960 245 [128] 2018
Plocamium cartilagineum 171,392 197 (coding) [117] 2016
Porphyra pulchra 194,175 251 [122] 2016 Bangiales
Porphyra purpurea 191,028 253 [129] 1993 Bangiales
Porphyra umbilicalis 190,173 250 [130] 2017 Bangiales
Porphyridium purpureum NIES 2140 217,694 260 [131] 2014
Porphyridium sordidum 259,429 227 [117] 2016
Pyropia fucicola 187,282 [132] 2015 Partial genome
Pyropia haitanensis PH 38 195,597 254 [133] 2013
Pyropia kanakaensis 189,931 [132] 2015 Partial genome
Pyropia perforata 189,789 247 [132] 2015
Pyropia yezoensis 191,952 264 [133] 2013
Rhodochaete parvula 221,665 195 (coding) [117] 2016
Rhodymenia pseudopalmata 194,153 201 (coding) [117] 2016
Riquetophycus sp. 180,384 202 (coding) [117] 2016
Schimmelmannia schousboei 181,030 202 (coding) [117] 2016
Schizymenia dubyi 183,959 204 (coding) [117] 2016
Sebdenia flabellata 192,140 205 (coding) [117] 2016
Sporolithon durum 191,464 239 [122] 2016
Thorea hispida 175,193 228 [128] 2018
Vertebrata lanosa 167,158 192 [134] 2015 Also assigned to genus Polysiphonia

Glaucophytes

Sequenced Plastomes
Species Variety Size (bp) Genes Reference
Cyanophora paradoxa [135]

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 Size (bp) Genes Reference Notes
Chromera velia
Chroomonas mesostigmatica CCMP1168 139,403 189 [136]
Chroomonas placoidea CCAP978/8 139,432 186 [136] Contains 3 annotated pseudogenes
Cryptomonas curvata CNUKR 128,285 182 [136]
Cryptomonas paramecium CCAP977/2a 77,717 115 [137]
Emiliania huxleyi CCMP 373 105,309 154 [138]
Guillardia theta 121,524 167 [139]
Heterosigma akashiwo NIES 293 159,370 198 [140]
Odontella sinensis 119,704 175 [141]
Phaeodactylum tricornutum 117,369 170 [142]
Rhodomonas salina CCMP1319 135,854 183 [143]
Storeatula sp. CCMP1868 140,953 187 [136]
Teleaulax amphioxeia HACCP-CR01 129,772 179 [144]
Thalassiosira pseudonana 128,814 180 [142]

Chlorarachniophytes

Sequenced Plastomes
Species Variety Size (bp) Genes Reference
Bigelowiella natans 69,166 98 [145]
Gymnochlora stellata CCMP2053 67,451 97 [146]
Lotharella oceanica CCMP622 70,997 94 [147]
Lotharella vacuolata CCMP240 71,557 95 [146]
Partenskyella glossopodia RCC365 72,620 99 [146]

Euglenophytes

Sequenced Plastomes
Species Variety Size (bp) Genes Reference
Astasia longa 73.2kb 84
Euglena gracilis 143.2kb 128 [148]

Apicomplexans

Sequenced Plastomes
Species Variety Size (bp) Genes Reference
Chromera velia
Eimeria tenella Penn State 34.8kb 65 [149]
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 Size (bp) Genes Reference
Amorphochlora amoebiformis 373,958 340 [150]
Bigelowiella natans CCMP 621 442,036 426 (344 protein coding) [151][152]
Chroomonas mesostigmatica CCMP1168 702,852 581 (505 protein coding) [153]
Cryptomonas paramecium 487,066 519 (466 protein coding) [154]
Guillardia theta 672,788 743 (632 protein coding) [155]
Hemiselmis andersenii 571,872 525 (471 protein coding) [156]
Lotharellaoceanica 612,592 654 (608 protein coding) [157]
Lotharellavacuolata 431,876 359 [150]

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 Size (bp) Genes Reference
Paulinella chromatophora 1.02Mb 867

See also

References

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External links



  1. Dennis, R. D. (January 1976). "Insect morphogenetic hormones and developmental mechanisms in the nematode, Nematospiroides dubius". Comparative Biochemistry and Physiology. A, Comparative Physiology 53 (1): 53–56. doi:10.1016/s0300-9629(76)80009-6. ISSN 0300-9629. PMID 184.