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 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 |
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 |
|
|
|
|
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
- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010). "Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots". Proc. Natl. Acad. Sci. U.S.A. 107 (10): 4623–8. doi:10.1073/pnas.0907801107. PMC 2842043. PMID 20176954.
- ↑ Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B (February 2008). "Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis". Mol. Biol. Evol. 25 (2): 393–401. doi:10.1093/molbev/msm267. PMID 18056074.
- ↑ Plastid genome evolution of the non-photosynthetic liverwort Aneura mirabilis (Malmb.) Wickett & Goffinet (Aneuraceae)
- ↑ 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.
- ↑ K Ohyama, Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Chang Z, Aota SI, 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.
- ↑ Sugiura C, Kobayashi Y, Aoki S, Sugita C, 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". Nucleic Acids Res. 31 (18): 5324–31. doi:10.1093/nar/gkg726. PMC 203311. PMID 12954768.
- ↑ Wolf PG, Rowe CA, Sinclair RB, Hasebe M (2003). "Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L". DNA Res. 10 (2): 59–65. doi:10.1093/dnares/10.2.59. PMID 12755170.
- ↑ 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
- ↑ 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. doi:10.1640/0002-8444(2007)97[95:TCPGSO]2.0.CO;2.
- ↑ Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, Ellis MW, Mishler BD, Kelch DG, Olmstead RG, Boore JL (2005). "The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)". Gene 350 (2): 117–28. doi:10.1016/j.gene.2005.01.018. PMID 15788152.
- ↑ 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.
- ↑ Tsuji S, Ueda K, Nishiyama T, Hasebe M, Yoshikawa S, Konagaya A, Nishiuchi T, Yamaguchi K (2007). "The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses". J. Plant Res. 120 (2): 281–90. doi:10.1007/s10265-006-0055-y. PMID 17297557.
- ↑ 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. doi:10.1186/1471-2229-8-70. PMC 2443145. PMID 18570682.
- 1 2 3 4 5 6 7 Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL (2007). "Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns". Proc. Natl. Acad. Sci. U.S.A. 104 (49): 19369–74. doi:10.1073/pnas.0709121104. PMC 2148296. PMID 18048330.
- ↑ Wu CS, 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): 1366–79. doi:10.1093/molbev/msm059. PMID 17383970.
- 1 2 Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW (2005). "Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone". Mol. Biol. Evol. 22 (10): 1948–63. doi:10.1093/molbev/msi191. PMID 15944438.
- ↑ Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, 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. U.S.A. 91 (21): 9794–8. Bibcode:1994PNAS...91.9794W. doi:10.1073/pnas.91.21.9794. PMC 44903. PMID 7937893.
- ↑ McCoy SR, Kuehl JV, Boore JL, Raubeson LA (2008). "The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates". BMC Evol. Biol. 8: 130. doi:10.1186/1471-2148-8-130. PMC 2386820. PMID 18452621.
- 1 2 3 4 5 6 7 8 9 10 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)
- ↑ 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.
- ↑ Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (1999). "Complete structure of the chloroplast genome of Arabidopsis thaliana". DNA Res. 6 (5): 283–90. doi:10.1093/dnares/6.5.283. PMID 10574454.
- ↑ 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". Mol. Biol. Evol. 19 (9): 1602–12. doi:10.1093/oxfordjournals.molbev.a004222. PMID 12200487.
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