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 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.
Plants
Bryophytes s.l.
Ferns and Lycophytes
Gymnosperms
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 |
Bryopsis plumosa |
|
106,859 |
115 |
[70] |
Chaetosphaeridium globosum |
|
131,183 |
124 |
[71] |
Chara vulgaris |
|
|
|
|
Chlamydomonas reinhardtii |
|
203,395 |
99 |
|
Chlorella vulgaris |
|
150,613 |
209 |
[72] |
Chlorokybus atmophyticus |
|
201,763 |
70 |
[73] |
Dunaliella salina |
CCAP 19/18 |
269,044 |
102 |
[74] |
Emiliania huxleyi |
|
105,309 |
150 |
|
Helicosporidium |
|
37,454 |
54 |
[75] |
Leptosira terrestris |
|
195,081 |
117 |
[76] |
Mesostigma viride |
|
42,424 |
|
|
Monomastix |
|
114,528 |
94 |
[77] |
Nephroselmis olivacea |
|
200,799 |
127 |
[78] |
Oedogonium cardiacum |
|
196,547 |
103 |
[79] |
Oltmannsiellopsis viridis |
|
151,933 |
105 |
[80] |
Ostreococcus tauri |
|
71,666 |
86 |
[81] |
Pseudendoclonium akinetum |
|
195,867 |
105 |
[82] |
Pycnococcus provasolii |
|
80,211 |
98 |
[77] |
Pyramimonas parkeae |
|
101,605 |
110 |
[77] |
Scenedesmus obliquus |
|
161,452 |
96 |
[83] |
Staurastrum punctulatum |
|
|
|
[84] |
Stigeoclonium helveticum |
|
223,902 |
97 |
[85] |
Tydemania expeditionis |
|
105,200 |
125 |
[70] |
Ulva sp. |
UNA00071828 |
99,983 |
102 |
[86] |
Volvox carteri |
|
420,650 |
91 |
[87] |
Zygnema circumcarinatum |
|
|
|
|
Glaucophytes
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.
Chlorarachniophytes
Apicomplexans
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.
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.)
See also
References
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External links
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Plastid genome evolution of the non-photosynthetic liverwort Aneura mirabilis (Malmb.) Wickett & Goffinet (Aneuraceae)
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 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
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 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.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 14.0 14.1 14.2 14.3 14.4 14.5 14.6 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 16.0 16.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 19.0 19.1 19.2 19.3 19.4 19.5 19.6 19.7 19.8 19.9 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)
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 23.0 23.1 23.2 23.3 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 30.0 30.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 33.0 33.1 33.2 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 40.0 40.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 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
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 47.0 47.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 49.0 49.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 51.0 51.1 51.2 51.3 51.4 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 52.0 52.1 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.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 58.0 58.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Gerald A. Tuskan, et alii (110 authors). 2006. "The genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)". Science 313 (5793):1596-1604.
- ↑ 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)
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 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
- ↑ 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
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 70.0 70.1 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ 77.0 77.1 77.2 Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ E. Virginia Armbrust, et alii (42 authors). 2004. "The Genome of the Diatom Thalassiosira pseudonana: Ecology, Evolution, and Metabolism". Science 306(5693):79-86.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.
- ↑ Lua error in package.lua at line 80: module 'strict' not found.