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.
Ferns and Lycophytes
Gymnosperms
Sequenced Plastomes
Species
Variety
Size (
bp )
Genes
Reference
Family
Notes
Cryptomeria japonica
131,810
114
[18]
Cupressaceae
Cycas
micronesica
[19]
Cycadaceae
Cycas taitungensis
163,403
133
[20]
Cycadaceae
Ephedra
equisetina
Ephedraceae
Ginkgo biloba
156,945
134
[21]
Ginkgoaceae
Gnetum
parvifolium
Gnetaceae
Picea engelmannii
Se404-851
123,542
114
[22]
Pinaceae
Picea glauca
PG29
123,266
114
[23]
Pinaceae
Picea glauca
WS77111
123,421
114
[24]
Pinaceae
Picea sitchensis
Q903
124,049
114
[25]
Pinaceae
Pinus
koraiensis
116,866
Pinaceae
Pinus thunbergii
119,707
[26]
Pinaceae
Podocarpus
macrophyllus
Podocarpaceae
Welwitschia mirabilis
119,726
101
[27]
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
[19]
2007
Acoraceae
Agrostis stolonifera
135,584
110
[28]
2010
Poaceae
Alniphyllum eberhardtii
155,384
113
[29]
2017
Styracaceae
Alstroemeria aurea
155,510
112
[30]
2013
Alstroemeriaceae
Amborella trichopoda
162,686
[31]
2003
Amborellaceae
Anethum graveolens
153,356
[19]
2007
Apiaceae
Arabidopsis thaliana
154,478
[32]
1999
Brassicaceae
Atropa belladonna
156,687
[33]
2002
Solanaceae
Brachypodium distachyon
135,199
110
[28]
2010
Poaceae
Buxus microphylla
159,010
113
[34]
2007
Buxaceae
Calycanthus floridus var. glaucus
153,337
115
[35]
2003
Calycanthaceae
Carpinus tientaiensis
160,104
114
[36]
2017
Betulaceae
Chloranthus spicatus
157,772
113
[34]
2007
Chloranthaceae
Citrus sinensis var. 'Ridge Pineapple'
155,189
[37]
2006
Rutaceae
Cocos nucifera
154,731
130
[38]
2013
Arecaceae
Coffea arabica
155,189
[39]
2007
Rubiaceae
Coix lacryma-jobi
140,745
[40]
2009
Poaceae
Conopholis americana
45,673
42
[41]
2013
Orobanchaceae
Non-photosynthetic parasite
Cucumis sativus
155,293
[42]
2007
Cucurbitaceae
Cuscuta exaltata
125,373
[43]
2007
Convolvulaceae
Cuscuta gronovii
86,744
86
[44]
2007
Convolvulaceae
Cuscuta reflexa
121,521
98
[44]
2007
Convolvulaceae
Cypripedium formosanum
178,131
[45]
2015
Orchidaceae
Cytinus hypocistis
19,400
23
[46]
2016
Cytinaceae
Holoparasitic
Daucus carota
155,911
[47]
2006
Apiaceae
Dioscorea elephantipes
152,609
112
[34]
2007
Dioscoreaceae
Drimys granadensis
160,604
113
[48]
2006
Winteraceae
Epifagus virginiana
70,028
42
[49]
1992
Orobanchaceae
Epipogium aphyllum
30,650
27
[50]
2015
Orchidaceae
Mycoheterotrophic
Epipogium roseum
19,047
29
[50]
2015
Orchidaceae
Mycoheterotrophic
Erodium carvifolium
116,935
107
[51]
2016
Geraniaceae
Erodium chrysanthum
168,946
96
[51]
2016
Geraniaceae
Erodium texanum
130,812
106
[52]
2011
Geraniaceae
Eucalyptus globulus subsp. globulus
160,286
[53]
2005
Myrtaceae
Fagopyrum esculentum ssp. ancestrale
159,599
[54]
2008
Polygonaceae
Geranium palmatum
155,794
105
[52]
2011
Geraniaceae
Glycine max
152,218
[55]
2005
Fabaceae
Gossypium barbadense
160,317
114
[56]
2006
Malvaceae
Gossypium hirsutum
160,301
[57]
2006
Malvaceae
Helianthus annuus
151,104
[58]
2007
Asteraceae
Hordeum vulgare subsp. vulgare
136,482
110
[28]
2010
Poaceae
Hydnora visseri
27,233
24
[59]
2016
Aristolochiaceae
Non-photosynthetic holoparasite
Illicium oligandrum
148,552
113
[34]
2007
Schisandraceae (
sensu
APG III )
Ipomoea purpurea
162,046
[43]
2007
Convolvulaceae
Jasminum nudiflorum
165,121
[60]
2007
Oleaceae
Juglans regia
160,367
129
[61]
2017
Juglandaceae
Lactuca sativa
152,765
[58]
2007
Asteraceae
Lemna minor
165,955
[62]
2008
Araliaceae
Licania alba
162,467
112
[63]
2014
Chrysobalanaceae
Lilium longiflorum
152,793
114
[30]
2013
Liliaceae
Liriodendron tulipifera
159,866
[48]
[64]
2006
Magnoliaceae
Lolium perenne
135,282
110
[28]
2010
Poaceae
Lonicera japonica
155,078
[1]
2010
Caprifoliaceae
Lotus japonicus
150,519
[65]
2000
Fabaceae
Manihot esculenta
161,453
[66]
2008
Euphorbiaceae
Monotropa hypopitys
35,336
45
[67]
2016
Ericaceae
Mycoheterotrophic
Monsonia speciosa
128,787
106
[52]
2011
Geraniaceae
Morus indica
156,599
[68]
2006
Moraceae
Musa balbisiana
169,503
113
[69]
2016
Musaceae
Nandina domestica
156,599
[70]
2006
Berberidaceae
Neottia nidus-avis
92,060
56
[71]
2011
Orchidaceae
Mycoheterotrophic
Nelumbo nucifera
163,330
[1]
2010
Nelumbonaceae
Nicotiana tabacum
155,943
113
[72]
1986
Solanaceae
Nuphar advena
160,866
117
[73]
2007
Nymphaeaceae
Nymphaea alba
159,930
[74]
2004
Nymphaeaceae
Oenothera argillicola strain Douthat 1
165,055
113
[75]
2008
Onagraceae
Oenothera biennis strain suaveolens Grado
164,807
113
[75]
2008
Onagraceae
Oenothera elata subsp. hookeri strain johansen Standard
165,728
113
[75]
2008
Onagraceae
Oenothera glazioviana strain r /r -lamarckiana Sweden
165,225
113
[75]
2008
Onagraceae
Oenothera parviflora strain atrovirens Standard
163,365
113
[75]
2008
Onagraceae
Oryza sativa indica 93-11
134,496
[76]
2005
Poaceae
Oryza sativa japonica Nipponbare
134,551
110
[77]
[28]
1989
Poaceae
Oryza sativa japonica PA64S
134,551
[76]
2005
Poaceae
Osyris alba
147,253
101
[78]
2015
Santalaceae
Hemiparasitic
Panax ginseng
156,318
[79]
2004
Araliaceae
Pelargonium × hortorum
217,942
[80]
2006
Geraniaceae
Petrosavia stellaris
103,835
58
[81]
2014
Petrosaviaceae
Mycoheterotrophic
Phalaenopsis aphrodite subsp. formosana
148,964
[82]
2006
Orchidaceae
Phaseolus vulgaris 'Negro Jamapa'
150,285
[83]
2007
Fabaceae
Pilostyles aethiopica
11,348
5
[84]
2016
Apodanthaceae
Endo-holoparasite
Pilostyles hamiltonii
15,167
5
[84]
2016
Apodanthaceae
Endo-holoparasite
Piper cenocladum
160,624
113
[48]
2006
Piperaceae
Platanus occidentalis
161,791
[70]
2006
Platanaceae
Populus alba
156,505
[85]
2006
Salicaceae
Ranunculus macranthus
155,158
117
[73]
2007
Ranunculaceae
Rhizanthella gardneri
59,190
33
[86]
2011
Orchidaceae
Subterranean
mycoheterotroph
Saccharum officinarum
141,182
110
[28]
2010
Poaceae
Sciaphila densiflora
21,485
28
[87]
2015
Triuridaceae
Mycoheterotrophic
Solanum tuberosum
155,298
[88]
2006
Solanaceae
Sorghum bicolor
140,754
110
[28]
2010
Poaceae
Spinacia oleracea
150,725
[89]
2001
Amaranthaceae
Trachelium caeruleum
162,321
[90]
2008
Campanulaceae
Trifolium subterraneum
144,763
111
[91]
2008
Fabaceae
Triticum aestivum cv. Chinese Spring
134,545
110
[92]
[93]
[28]
2000
Poaceae
Typha latifolia
165,572
113
[28]
2010
Typhaceae
Vaccinium macrocarpon
176,045
147
[94]
2013
Ericaceae
Viscum album
128,921
96
[78]
2015
Viscaceae
Hemiparasitic
Viscum minimum
131,016
99
[78]
2015
Viscaceae
Hemiparasitic
Vitis vinifera
160,928
[95]
2006
Vitaceae
Yucca schidigera
156,158
[21]
2005
Asparagaceae (
sensu
APG III )
Zea mays
140,384
110
[96]
[28]
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
[97]
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
[19]
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
[19]
2007
Passifloraceae
Phoradendron leucarpum
[1]
2010
Viscaceae
Plumbago auriculata
[1]
2010
Plumbaginaceae
Populus trichocarpa
[98]
2006
Salicaceae
Quercus nigra
[1]
2010
Fagaceae
Rhododendron simsii
[1]
2010
Ericaceae
Scaevola aemula
[19]
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
[99]
Green algae
Sequenced Plastomes
Species
Variety
Size (
bp )
Genes
Reference
Bryopsis plumosa
106,859
115
[100]
Chaetosphaeridium globosum
131,183
124
[101]
Chara vulgaris
Chlamydomonas reinhardtii
203,395
99
Chlorella
vulgaris
150,613
209
[102]
Chlorokybus atmophyticus
201,763
70
[103]
Dunaliella salina
CCAP 19/18
269,044
102
[104]
Emiliania huxleyi
105,309
150
Helicosporidium
37,454
54
[105]
Leptosira
terrestris
195,081
117
[106]
Mesostigma viride
42,424
Monomastix
114,528
94
[107]
Nephroselmis
olivacea
200,799
127
[108]
Oedogonium
cardiacum
196,547
103
[109]
Oltmannsiellopsis
viridis
151,933
105
[110]
Ostreococcus
tauri
71,666
86
[111]
Pseudendoclonium
akinetum
195,867
105
[112]
Pycnococcus provasolii
80,211
98
[107]
Pyramimonas parkeae
101,605
110
[107]
Scenedesmus
obliquus
161,452
96
[113]
Staurastrum
punctulatum
[114]
Stigeoclonium
helveticum
223,902
97
[115]
Tydemania expeditionis
105,200
125
[100]
Ulva sp.
UNA00071828
99,983
102
[116]
Volvox carteri
420,650
91
[117]
Zygnema
circumcarinatum
Sequenced Plastomes
Species
Variety
Size (
bp )
Genes
Reference
Year
Taxon
Notes
Ahnfeltia plicata
190,451
205 (coding)
[118]
2016
Ahnfeltiales
Apophlaea
sinclairii
182,437
189 (coding)
[118]
2016
Hildenbrandiales
Asparagopsis taxiformis
177,091
203 (coding)
[118]
2016
Bangiopsis subsimplex
204,784
194 (coding)
[118]
2016
Calliarthron tuberculosum
178,981
238
[119]
2013
Ceramium
japonicum
171,634
199 (coding)
[118]
2016
Chondrus crispus
180,086
240
[119]
2013
Gigartinales
Cyanidioschyzon merolae
10D
149,987
243
[120]
2003
Cyanidium
caldarium
RK1
164,921
230
[121]
2000
Erythrotrichia carnea
210,691
191 (coding)
[118]
2016
Galdieria sulphuraria
074W
167,741
233
[122]
2015
Gelidium elegans
174,748
234
[123]
2016
Gelidium sinicola
UC276620
177,095
232
[124]
2019
May be synonymous with G. coulteri
Gelidium vagum
179,853
234
[123]
2016
Gracilaria changii
183,855
231
[125]
2018
Gracilariales
Gracilaria chorda
182,459
201 (coding)
[118]
2016
Gracilariales
Gracilaria salicornia
179,757
235
[126]
2014
Gracilariales
Gracilaria
tenuistipitata
var. liui
183,883
238
[127]
2004
Gracilariales
Gracilaria vermiculophylla
180,254
239
unpublished
Gracilariales
Grateloupia filicina
195,990
265
unpublished
Grateloupia taiwanensis
191,270
266
[128]
2013
Hildenbrandia rivularis
189,725
184 (coding)
[118]
2016
Hildenbrandia rubra
180,141
190 (coding)
[118]
2016
Kumanoa americana
184,025
234
[129]
2018
Palmaria palmata
192,960
245
[129]
2018
Plocamium cartilagineum
171,392
197 (coding)
[118]
2016
Porphyra pulchra
194,175
251
[123]
2016
Bangiales
Porphyra purpurea
191,028
253
[130]
1993
Bangiales
Porphyra umbilicalis
190,173
250
[131]
2017
Bangiales
Porphyridium purpureum
NIES 2140
217,694
260
[132]
2014
Porphyridium sordidum
259,429
227
[118]
2016
Pyropia
fucicola
187,282
[133]
2015
Partial genome
Pyropia haitanensis
PH 38
195,597
254
[134]
2013
Pyropia
kanakaensis
189,931
[133]
2015
Partial genome
Pyropia perforata
189,789
247
[133]
2015
Pyropia
yezoensis
191,952
264
[134]
2013
Rhodochaete
parvula
221,665
195 (coding)
[118]
2016
Rhodymenia
pseudopalmata
194,153
201 (coding)
[118]
2016
Riquetophycus sp.
180,384
202 (coding)
[118]
2016
Schimmelmannia schousboei
181,030
202 (coding)
[118]
2016
Schizymenia dubyi
183,959
204 (coding)
[118]
2016
Sebdenia flabellata
192,140
205 (coding)
[118]
2016
Sporolithon durum
191,464
239
[123]
2016
Thorea hispida
175,193
228
[129]
2018
Vertebrata lanosa
167,158
192
[135]
2015
Also assigned to genus
Polysiphonia
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.
Sequenced Plastomes
Species
Variety
Size (
bp )
Genes
Reference
Notes
Chromera velia
Chroomonas mesostigmatica
CCMP1168
139,403
189
[137]
Chroomonas placoidea
CCAP978/8
139,432
186
[137]
Contains 3 annotated pseudogenes
Cryptomonas curvata
CNUKR
128,285
182
[137]
Cryptomonas paramecium
CCAP977/2a
77,717
115
[138]
Emiliania huxleyi
CCMP 373
105,309
154
[139]
Guillardia
theta
121,524
167
[140]
Heterosigma akashiwo
NIES 293
159,370
198
[141]
Odontella sinensis
119,704
175
[142]
Phaeodactylum tricornutum
117,369
170
[143]
Rhodomonas
salina
CCMP1319
135,854
183
[144]
Storeatula sp.
CCMP1868
140,953
187
[137]
Teleaulax amphioxeia
HACCP-CR01
129,772
179
[145]
Thalassiosira
pseudonana
128,814
180
[143]
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
^
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q
r
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t
u
v
w
x Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (March 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): 4623–8.
Bibcode :
2010PNAS..107.4623M .
doi :
10.1073/pnas.0907801107 .
PMC
2842043 .
PMID
20176954 .
^
"Index of /refseq/release/plastid" . ftp.ncbi.nlm.nih.gov . Retrieved 2017-01-08 .
^ 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" . Molecular Biology and Evolution . 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)
^ Kugita M, Kaneko A, Yamamoto Y, Takeya Y, Matsumoto T, Yoshinaga K (January 2003).
"The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants" . Nucleic Acids Research . 31 (2): 716–21.
doi :
10.1093/nar/gkg155 .
PMC
140519 .
PMID
12527781 .
^ 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.
Bibcode :
1986Natur.322..572O .
doi :
10.1038/322572a0 .
S2CID
4311952 .
^ Villarreal JC, Forrest LL, Wickett N, Goffinet B (March 2013). "The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain". American Journal of Botany . 100 (3): 467–77.
doi :
10.3732/ajb.1200429 .
PMID
23416362 .
^ Grosche C, Funk HT, Maier UG, Zauner S (2012).
"The chloroplast genome of Pellia endiviifolia: gene content, RNA-editing pattern, and the origin of chloroplast editing" . Genome Biology and Evolution . 4 (12): 1349–57.
doi :
10.1093/gbe/evs114 .
PMC
3542565 .
PMID
23221608 .
^ Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M (September 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): 5324–31.
doi :
10.1093/nar/gkg726 .
PMC
203311 .
PMID
12954768 .
^ Laura L. Forrest; Norman J. Wickett, Cymon J. Cox & Bernard Goffinet (2011).
"Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure" (PDF) . Plant Ecology and Evolution . 144 (1): 29–43.
doi :
10.5091/plecevo.2011.535 .
hdl :
10400.1/5518 .
^ Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KD, Wolf PG, Duffy AM, Karol KG (February 2010).
"Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes" . BMC Genomics . 11 : 143.
doi :
10.1186/1471-2164-11-143 .
PMC
2841679 .
PMID
20187961 .
^ Wolf PG, Rowe CA, Sinclair RB, Hasebe M (April 2003).
"Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L" . DNA Research . 10 (2): 59–65.
doi :
10.1093/dnares/10.2.59 .
PMID
12755170 .
^ Gao L, Yi X, Yang YX, Su YJ, Wang T (June 2009).
"Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes" . BMC Evolutionary Biology . 9 : 130.
doi :
10.1186/1471-2148-9-130 .
PMC
2706227 .
PMID
19519899 .
^ Roper JM, Hansen SK, Wolf PG, Karol KG, Mandoli DF, Everett KD, Kuehl J, Boore JL (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 (May 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 .
^ Wakasugi, T (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 (March 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): 281–90.
doi :
10.1007/s10265-006-0055-y .
PMID
17297557 .
S2CID
7691300 .
^ Hirao T, Watanabe A, Kurita M, Kondo T, Takata K (June 2008).
"Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species" . BMC Plant Biology . 8 : 70.
doi :
10.1186/1471-2229-8-70 .
PMC
2443145 .
PMID
18570682 .
^
a
b
c
d
e
f 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 (December 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 of the United States of America . 104 (49): 19369–74.
Bibcode :
2007PNAS..10419369J .
doi :
10.1073/pnas.0709121104 .
PMC
2148296 .
PMID
18048330 .
^ Wu CS, Wang YN, Liu SM, Chaw SM (June 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" . Molecular Biology and Evolution . 24 (6): 1366–79.
doi :
10.1093/molbev/msm059 .
PMID
17383970 .
^
a
b Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW (October 2005).
"Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone" . Molecular Biology and Evolution . 22 (10): 1948–63.
doi :
10.1093/molbev/msi191 .
PMID
15944438 .
^ Lin, Diana; Coombe, Lauren; Jackman, Shaun D.; Gagalova, Kristina K.; Warren, René L.; Hammond, S. Austin; McDonald, Helen; Kirk, Heather; Pandoh, Pawan; Zhao, Yongjun; Moore, Richard A. (2019-06-13). Stajich, Jason E. (ed.).
"Complete Chloroplast Genome Sequence of an Engelmann Spruce ( Picea engelmannii , Genotype Se404-851) from Western Canada" . Microbiology Resource Announcements . 8 (24): e00382–19, /mra/8/24/MRA.00382–19.atom.
doi :
10.1128/MRA.00382-19 .
ISSN
2576-098X .
PMC
6588038 .
PMID
31196920 .
^ Jackman, Shaun D.; Warren, René L.; Gibb, Ewan A.; Vandervalk, Benjamin P.; Mohamadi, Hamid; Chu, Justin; Raymond, Anthony; Pleasance, Stephen; Coope, Robin; Wildung, Mark R.; Ritland, Carol E. (January 2016).
"Organellar Genomes of White Spruce ( Picea glauca ): Assembly and Annotation" . Genome Biology and Evolution . 8 (1): 29–41.
doi :
10.1093/gbe/evv244 .
ISSN
1759-6653 .
PMC
4758241 .
PMID
26645680 .
^ Lin, Diana; Coombe, Lauren; Jackman, Shaun D.; Gagalova, Kristina K.; Warren, René L.; Hammond, S. Austin; Kirk, Heather; Pandoh, Pawan; Zhao, Yongjun; Moore, Richard A.; Mungall, Andrew J. (2019-06-06). Rokas, Antonis (ed.).
"Complete Chloroplast Genome Sequence of a White Spruce ( Picea glauca , Genotype WS77111) from Eastern Canada" . Microbiology Resource Announcements . 8 (23): e00381–19, /mra/8/23/MRA.00381–19.atom.
doi :
10.1128/MRA.00381-19 .
ISSN
2576-098X .
PMC
6554609 .
PMID
31171622 .
^ Coombe, Lauren; Warren, René L.; Jackman, Shaun D.; Yang, Chen; Vandervalk, Benjamin P.; Moore, Richard A.; Pleasance, Stephen; Coope, Robin J.; Bohlmann, Joerg; Holt, Robert A.; Jones, Steven J. M. (2016-09-15). Budak, Hikmet (ed.).
"Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data" . PLOS ONE . 11 (9): e0163059.
Bibcode :
2016PLoSO..1163059C .
doi :
10.1371/journal.pone.0163059 .
ISSN
1932-6203 .
PMC
5025161 .
PMID
27632164 .
^ Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M (October 1994).
"Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii" . Proceedings of the National Academy of Sciences of the United States of America . 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 (May 2008).
"The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates" . BMC Evolutionary Biology . 8 : 130.
doi :
10.1186/1471-2148-8-130 .
PMC
2386820 .
PMID
18452621 .
^
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)
^ Yan M, Moore MJ, Meng A, Yao X, Wang H (2016-09-21). "The first complete plastome sequence of the basal asterid family Styracaceae (Ericales) reveals a large inversion". Plant Systematics and Evolution . 303 (1): 61–70.
doi :
10.1007/s00606-016-1352-0 .
ISSN
0378-2697 .
S2CID
25942874 .
^
a
b Kim JS, Kim JH (2013-06-18).
"Comparative genome analysis and phylogenetic relationship of order Liliales insight from the complete plastid genome sequences of two Lilies (Lilium longiflorum and Alstroemeria aurea)" . PLOS ONE . 8 (6): e68180.
Bibcode :
2013PLoSO...868180K .
doi :
10.1371/journal.pone.0068180 .
PMC
3688979 .
PMID
23950788 .
^ Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH (September 2003).
"Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm" . Molecular Biology and Evolution . 20 (9): 1499–505.
doi :
10.1093/molbev/msg159 .
PMID
12832641 .
^ Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (October 1999).
"Complete structure of the chloroplast genome of Arabidopsis thaliana" . DNA Research . 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 (September 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): 1602–12.
doi :
10.1093/oxfordjournals.molbev.a004222 .
PMID
12200487 .
S2CID
1111063 .
^
a
b
c
d Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK (November 2007). "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): 547–63.
doi :
10.1016/j.ympev.2007.06.004 .
PMID
17644003 .
^ Goremykin V, Hirsch-Ernst KI, Wölfl S, Hellwig FH (2003). "The chloroplast genome of the basal angiosperm Calycanthus fertilis – structural and phylogenetic analyses". Plant Systematics and Evolution . 242 (1–4): 119–135.
doi :
10.1007/s00606-003-0056-4 .
S2CID
44377635 .
^ Yang Y, Wang M, Lu Z, Xie X, Feng S (2017-01-04). "Characterization of the complete chloroplast genome of Carpinus tientaiensis ". Conservation Genetics Resources . 9 (2): 339–341.
doi :
10.1007/s12686-016-0668-y .
ISSN
1877-7252 .
S2CID
5184815 .
^ Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H (September 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.
doi :
10.1186/1471-2229-6-21 .
PMC
1599732 .
PMID
17010212 .
^ Huang YY, Matzke AJ, Matzke M (2013-08-30).
"Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera)" . PLOS ONE . 8 (8): e74736.
Bibcode :
2013PLoSO...874736H .
doi :
10.1371/journal.pone.0074736 .
PMC
3758300 .
PMID
24023703 .
^ Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H (March 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): 339–53.
doi :
10.1111/j.1467-7652.2007.00245.x .
PMC
3473179 .
PMID
17309688 .
^ Leseberg CH, Duvall MR (October 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): 311–8.
Bibcode :
2009JMolE..69..311L .
doi :
10.1007/s00239-009-9275-9 .
PMID
19777151 .
S2CID
24418374 .
^ Wicke S, Müller KF, de Pamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM (October 2013).
"Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family" . The Plant Cell . 25 (10): 3711–25.
doi :
10.1105/tpc.113.113373 .
PMC
3877813 .
PMID
24143802 .
^ Plader W, Yukawa Y, Sugiura M, Malepszy S (2007).
"The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: its composition and comparative analysis" . Cellular & Molecular Biology Letters . 12 (4): 584–94.
doi :
10.2478/s11658-007-0029-7 .
PMC
6275786 .
PMID
17607527 .
^
a
b McNeal JR, Kuehl JV, Boore JL, de Pamphilis CW (October 2007).
"Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta" . BMC Plant Biology . 7 : 57.
doi :
10.1186/1471-2229-7-57 .
PMC
2216012 .
PMID
17956636 .
^
a
b Funk HT, Berg S, Krupinska K, Maier UG, Krause K (August 2007).
"Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii" . BMC Plant Biology . 7 : 45.
doi :
10.1186/1471-2229-7-45 .
PMC
2089061 .
PMID
17714582 .
^ Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GK, Albert VA, Chou ML, Chen CY, Shih MC (March 2015).
"The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family" . Scientific Reports . 5 : 9040.
Bibcode :
2015NatSR...5E9040L .
doi :
10.1038/srep09040 .
PMC
4356964 .
PMID
25761566 .
^ Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S (July 2016).
"Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae)" . Annals of Botany . 118 (5): 885–896.
doi :
10.1093/aob/mcw135 .
PMC
5055816 .
PMID
27443299 .
^ Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (August 2006).
"Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms" . BMC Genomics . 7 : 222.
doi :
10.1186/1471-2164-7-222 .
PMC
1579219 .
PMID
16945140 .
^
a
b
c Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK (October 2006).
"Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids" . BMC Evolutionary Biology . 6 : 77.
doi :
10.1186/1471-2148-6-77 .
PMC
1626487 .
PMID
17020608 .
^ Wolfe KH, Morden CW, Palmer JD (November 1992).
"Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant" . Proceedings of the National Academy of Sciences of the United States of America . 89 (22): 10648–52.
Bibcode :
1992PNAS...8910648W .
doi :
10.1073/pnas.89.22.10648 .
PMC
50398 .
PMID
1332054 .
^
a
b Schelkunov MI, Shtratnikova VY, Nuraliev MS, Selosse MA, Penin AA, Logacheva MD (January 2015).
"Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum" . Genome Biology and Evolution . 7 (4): 1179–91.
doi :
10.1093/gbe/evv019 .
PMC
4419786 .
PMID
25635040 .
^
a
b Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, Ruhlman TA (June 2016).
"Variable presence of the inverted repeat and plastome stability in Erodium" . Annals of Botany . 117 (7): 1209–20.
doi :
10.1093/aob/mcw065 .
PMC
4904181 .
PMID
27192713 .
^
a
b
c Guisinger MM, Kuehl JV, Boore JL, Jansen RK (January 2011).
"Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage" . Molecular Biology and Evolution . 28 (1): 583–600.
doi :
10.1093/molbev/msq229 .
PMID
20805190 .
^ Steane DA (2005).
"Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae)" . DNA Research . 12 (3): 215–20.
doi :
10.1093/dnares/dsi006 .
PMID
16303753 .
^ Logacheva MD, Samigullin TH, Dhingra A, Penin AA (May 2008).
"Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale -a wild ancestor of cultivated buckwheat" . BMC Plant Biology . 8 : 59.
doi :
10.1186/1471-2229-8-59 .
PMC
2430205 .
PMID
18492277 .
^ Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, Jansen RK (September 2005). "Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes". Plant Molecular Biology . 59 (2): 309–22.
doi :
10.1007/s11103-005-8882-0 .
PMID
16247559 .
S2CID
3332004 .
^ Ibrahim RI, Azuma J, Sakamoto M (October 2006).
"Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants" . Genes & Genetic Systems . 81 (5): 311–21.
doi :
10.1266/ggs.81.311 .
PMID
17159292 .
^ Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (March 2006).
"The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms" . BMC Genomics . 7 : 61.
doi :
10.1186/1471-2164-7-61 .
PMC
1513215 .
PMID
16553962 .
^
a
b Timme RE, Kuehl JV, Boore JL, Jansen RK (March 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): 302–12.
doi :
10.3732/ajb.94.3.302 .
PMID
21636403 .
^ Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW (January 2016).
"Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae)" . Genome Biology and Evolution . 8 (2): 345–63.
doi :
10.1093/gbe/evv256 .
PMC
4779604 .
PMID
26739167 .
^ Lee HL, Jansen RK, Chumley TW, Kim KJ (May 2007).
"Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions" . Molecular Biology and Evolution . 24 (5): 1161–80.
doi :
10.1093/molbev/msm036 .
PMID
17329229 .
^ Hu Y, Woeste KE, Zhao P (2017-01-01).
"Juglans and Their Contribution to Chloroplast Phylogeny" . Frontiers in Plant Science . 7 : 1955.
doi :
10.3389/fpls.2016.01955 .
PMC
5216037 .
PMID
28111577 .
^ Mardanov AV, Ravin NV, Kuznetsov BB, Samigullin TH, Antonov AS, Kolganova TV, Skyabin KG (June 2008). "Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms". Journal of Molecular Evolution . 66 (6): 555–64.
Bibcode :
2008JMolE..66..555M .
doi :
10.1007/s00239-008-9091-7 .
PMID
18463914 .
S2CID
10044367 .
^ Malé PJ, Bardon L, Besnard G, Coissac E, Delsuc F, Engel J, Lhuillier E, Scotti-Saintagne C, Tinaut A, Chave J (September 2014). "Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family". Molecular Ecology Resources . 14 (5): 966–75.
doi :
10.1111/1755-0998.12246 .
PMID
24606032 .
S2CID
26777683 .
^ Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, Buzgo M, Landherr LL, Hu Y, DiLoreto DS, Ilut DC, Field D, Tanksley SD, Ma H, Claude (2008). "An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron". Tree Genetics & Genomes . 4 (3): 419–433.
doi :
10.1007/s11295-007-0120-2 .
S2CID
44266336 .
^ Kato T, Kaneko T, Sato S, Nakamura Y, Tabata S (December 2000).
"Complete structure of the chloroplast genome of a legume, Lotus japonicus" . DNA Research . 7 (6): 323–30.
doi :
10.1093/dnares/7.6.323 .
PMID
11214967 .
^ Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski C, Jansen RK (March 2008).
"The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron" . Theoretical and Applied Genetics . 116 (5): 723–37.
doi :
10.1007/s00122-007-0706-y .
PMC
2587239 .
PMID
18214421 .
^ Ravin NV, Gruzdev EV, Beletsky AV, Mazur AM, Prokhortchouk EB, Filyushin MA, Kochieva EZ, Kadnikov VV, Mardanov AV, Skryabin KG (November 2016).
"The loss of photosynthetic pathways in the plastid and nuclear genomes of the non-photosynthetic mycoheterotrophic eudicot Monotropa hypopitys" . BMC Plant Biology . 16 (Suppl 3): 238.
doi :
10.1186/s12870-016-0929-7 .
PMC
5123295 .
PMID
28105941 .
^ Ravi V, Khurana JP, Tyagi AK, Khurana P (2006). "The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis". Tree Genetics & Genomes . 3 (1): 49–59.
doi :
10.1007/s11295-006-0051-3 .
S2CID
22104273 .
^ Shetty SM, Md Shah MU, Makale K, Mohd-Yusuf Y, Khalid N, Othman RY (July 2016).
"Complete Chloroplast Genome Sequence of Corroborates Structural Heterogeneity of Inverted Repeats in Wild Progenitors of Cultivated Bananas and Plantains" . The Plant Genome . 9 (2).
doi :
10.3835/plantgenome2015.09.0089 .
PMID
27898825 .
^
a
b Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM, Soltis DE (August 2006).
"Rapid and accurate pyrosequencing of angiosperm plastid genomes" . BMC Plant Biology . 6 : 17.
doi :
10.1186/1471-2229-6-17 .
PMC
1564139 .
PMID
16934154 .
^ Logacheva MD, Schelkunov MI, Penin AA (2011-01-01).
"Sequencing and analysis of plastid genome in mycoheterotrophic orchid Neottia nidus-avis" . Genome Biology and Evolution . 3 : 1296–303.
doi :
10.1093/gbe/evr102 .
PMC
3228488 .
PMID
21971517 .
^ 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 BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (September 1986).
"The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression" . The EMBO Journal . 5 (9): 2043–2049.
doi :
10.1002/j.1460-2075.1986.tb04464.x .
PMC
1167080 .
PMID
16453699 .
^
a
b Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK (June 2007).
"Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus" . BMC Genomics . 8 : 174.
doi :
10.1186/1471-2164-8-174 .
PMC
1925096 .
PMID
17573971 .
^ Goremykin VV, Hirsch-Ernst KI, Wölfl S, Hellwig FH (July 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): 1445–54.
doi :
10.1093/molbev/msh147 .
PMID
15084683 .
^
a
b
c
d
e Greiner S, Wang X, Rauwolf U, Silber MV, Mayer K, Meurer J, Haberer G, Herrmann RG (April 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.
doi :
10.1093/nar/gkn081 .
PMC
2367718 .
PMID
18299283 .
^
a
b Yu J, Wang J, Lin W, Li S, Li H, Zhou J, et al. (February 2005).
"The Genomes of Oryza sativa: a history of duplications" . PLOS Biology . 3 (2): e38.
doi :
10.1371/journal.pbio.0030038 .
PMC
546038 .
PMID
15685292 .
^ Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY (June 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 & General Genetics . 217 (2–3): 185–94.
doi :
10.1007/BF02464880 .
PMID
2770692 .
S2CID
36458326 .
^
a
b
c Petersen G, Cuenca A, Seberg O (August 2015).
"Plastome Evolution in Hemiparasitic Mistletoes" . Genome Biology and Evolution . 7 (9): 2520–32.
doi :
10.1093/gbe/evv165 .
PMC
4607522 .
PMID
26319577 .
^ Kim KJ, Lee HL (August 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): 247–61.
doi :
10.1093/dnares/11.4.247 .
PMID
15500250 .
^ Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK (November 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): 2175–90.
doi :
10.1093/molbev/msl089 .
PMID
16916942 .
^ Logacheva MD, Schelkunov MI, Nuraliev MS, Samigullin TH, Penin AA (January 2014).
"The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements" . Genome Biology and Evolution . 6 (1): 238–46.
doi :
10.1093/gbe/evu001 .
PMC
3914687 .
PMID
24398375 .
^ Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chang CC, Chaw SM (February 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): 279–91.
doi :
10.1093/molbev/msj029 .
PMID
16207935 .
^ Guo X, Castillo-Ramírez S, González V, Bustos P, Fernández-Vázquez JL, Santamaría RI, Arellano J, Cevallos MA, Dávila G (July 2007).
"Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts" . BMC Genomics . 8 : 228.
doi :
10.1186/1471-2164-8-228 .
PMC
1940014 .
PMID
17623083 .
^
a
b Bellot S, Renner SS (December 2015).
"The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes" . Genome Biology and Evolution . 8 (1): 189–201.
doi :
10.1093/gbe/evv251 .
PMC
4758247 .
PMID
26660355 .
^ Okumura S, Sawada M, Park YW, Hayashi T, Shimamura M, Takase H, Tomizawa K (October 2006). "Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts". Transgenic Research . 15 (5): 637–46.
doi :
10.1007/s11248-006-9009-3 .
PMID
16952016 .
S2CID
39294451 .
^ Delannoy E, Fujii S, Colas des Francs-Small C, Brundrett M, Small I (July 2011).
"Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes" . Molecular Biology and Evolution . 28 (7): 2077–86.
doi :
10.1093/molbev/msr028 .
PMC
3112369 .
PMID
21289370 .
^ Lam VK, Soto Gomez M, Graham SW (July 2015).
"The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection" . Genome Biology and Evolution . 7 (8): 2220–36.
doi :
10.1093/gbe/evv134 .
PMC
4558852 .
PMID
26170229 .
^ Chung HJ, Jung JD, Park HW, Kim JH, Cha HW, Min SR, Jeong WJ, Liu JR (December 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): 1369–79.
doi :
10.1007/s00299-006-0196-4 .
PMID
16835751 .
S2CID
24055793 .
^ Schmitz-Linneweber C, Maier RM, Alcaraz JP, Cottet A, Herrmann RG, Mache R (February 2001). "The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization". Plant Molecular Biology . 45 (3): 307–15.
doi :
10.1023/A:1006478403810 .
PMID
11292076 .
S2CID
28271437 .
^ Haberle RC, Fourcade HM, Boore JL, Jansen RK (April 2008). "Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes". Journal of Molecular Evolution . 66 (4): 350–61.
Bibcode :
2008JMolE..66..350H .
CiteSeerX
10.1.1.174.5498 .
doi :
10.1007/s00239-008-9086-4 .
PMID
18330485 .
S2CID
18228097 .
^ Cai Z, et al. (2008). "Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions". J Mol Evol . 67 (6): 696–704.
Bibcode :
2008JMolE..67..696C .
doi :
10.1007/s00239-008-9180-7 .
PMID
19018585 .
S2CID
36486188 .
^ Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, et al. (2000). "Chinese Spring Wheat (Triticum aestivum L.) Chloroplast Genome: Complete Sequence and Contig Clones". Plant Molecular Biology Reporter . 18 (3): 243–253.
doi :
10.1007/BF02823995 .
S2CID
41773993 .
^ Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H, Tsunewaki K (January 2002). "Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA". Molecular Genetics and Genomics . 266 (5): 740–6.
doi :
10.1007/s00438-001-0606-9 .
PMID
11810247 .
S2CID
22434780 .
^ Fajardo D, Senalik D, Ames M, Zhu H, Steffan SA, Harbut R, Polashock J, Vorsa N, Gillespie E, Kron K, Zalapa JE (2013). "Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing". Tree Genetics & Genomes . 9 (2): 489–498.
doi :
10.1007/s11295-012-0573-9 .
S2CID
17130517 .
^ Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H (April 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.
doi :
10.1186/1471-2148-6-32 .
PMC
1479384 .
PMID
16603088 .
^ Maier RM, Neckermann K, Igloi GL, Kössel H (September 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): 614–28.
doi :
10.1006/jmbi.1995.0460 .
PMID
7666415 .
^ Moore MJ, Bell CD, Soltis PS, Soltis DE (December 2007).
"Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms" . Proceedings of the National Academy of Sciences of the United States of America . 104 (49): 19363–8.
Bibcode :
2007PNAS..10419363M .
doi :
10.1073/pnas.0708072104 .
PMC
2148295 .
PMID
18048334 .
^ Gerald A. Tuskan, et alii (110 authors). 2006. "The genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)". Science 313 (5793):1596-1604.
^ Nickrent DL, Malécot V, Vidal-Russell R, Der JP (2010). "A revised classification of Santalales". Taxon . 59 (2): 538–558.
doi :
10.1002/tax.592019 .
S2CID
85950875 .
^
a
b Leliaert F, Lopez-Bautista JM (March 2015).
"The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin" . BMC Genomics . 16 (1): 204.
doi :
10.1186/s12864-015-1418-3 .
PMC
4487195 .
PMID
25879186 .
^ 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" . Proceedings of the National Academy of Sciences of the United States of America . 99 (17): 11275–80.
Bibcode :
2002PNAS...9911275T .
doi :
10.1073/pnas.162203299 .
PMC
123247 .
PMID
12161560 .
^ Wakasugi T, Nagai T, Kapoor M, Sugita M, Ito M, Ito S, Tsudzuki J, Nakashima K, Tsudzuki T, Suzuki Y, Hamada A, Ohta T, Inamura A, Yoshinaga K, Sugiura M (May 1997).
"Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division" . Proceedings of the National Academy of Sciences of the United States of America . 94 (11): 5967–72.
Bibcode :
1997PNAS...94.5967W .
doi :
10.1073/pnas.94.11.5967 .
PMC
20890 .
PMID
9159184 .
^ Turmel M, Otis C, Lemieux C (May 2007).
"An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus" . BMC Genomics . 8 : 137.
doi :
10.1186/1471-2164-8-137 .
PMC
1894977 .
PMID
17537252 .
^ Smith DR, et al. (May 2010).
"The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA" . BMC Plant Biology . 10 : 83.
doi :
10.1186/1471-2229-10-83 .
PMC
3017802 .
PMID
20459666 .
^ de Koning AP, Keeling PJ (April 2006).
"The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured" . BMC Biology . 4 : 12.
doi :
10.1186/1741-7007-4-12 .
PMC
1463013 .
PMID
16630350 .
^ de Cambiaire JC, Otis C, Turmel M, Lemieux C (July 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.
doi :
10.1186/1471-2164-8-213 .
PMC
1931444 .
PMID
17610731 .
^
a
b
c Turmel M, Gagnon MC, O'Kelly CJ, Otis C, Lemieux C (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): 631–48.
doi :
10.1093/molbev/msn285 .
PMID
19074760 .
^ 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" . Proceedings of the National Academy of Sciences of the United States of America . 96 (18): 10248–53.
Bibcode :
1999PNAS...9610248T .
doi :
10.1073/pnas.96.18.10248 .
PMC
17874 .
PMID
10468594 .
^ Brouard JS, Otis C, Lemieux C, Turmel M (June 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.
doi :
10.1186/1471-2164-9-290 .
PMC
2442088 .
PMID
18558012 .
^ Pombert JF, Lemieux C, Turmel M (February 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 Biology . 4 : 3.
doi :
10.1186/1741-7007-4-3 .
PMC
1402334 .
PMID
16472375 .
^ 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" . Molecular Biology and Evolution . 24 (4): 956–68.
doi :
10.1093/molbev/msm012 .
PMID
17251180 .
^ 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" . Molecular Biology and Evolution . 22 (9): 1903–18.
doi :
10.1093/molbev/msi182 .
PMID
15930151 .
^ de Cambiaire JC, Otis C, Lemieux C, Turmel M (April 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 Evolutionary Biology . 6 : 37.
doi :
10.1186/1471-2148-6-37 .
PMC
1513399 .
PMID
16638149 .
^ Turmel M, Otis C, Lemieux C (October 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 Biology . 3 : 22.
doi :
10.1186/1741-7007-3-22 .
PMC
1277820 .
PMID
16236178 .
^ 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". Molecular Genetics and Genomics . 276 (5): 464–77.
doi :
10.1007/s00438-006-0156-2 .
PMID
16944205 .
S2CID
19489840 .
^ Melton JT, Leliaert F, Tronholm A, Lopez-Bautista JM (2015).
"The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta)" . PLOS ONE . 10 (4): e0121020.
Bibcode :
2015PLoSO..1021020M .
doi :
10.1371/journal.pone.0121020 .
PMC
4388391 .
PMID
25849557 .
^ Smith DR, Lee RW (March 2009).
"The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA" . BMC Genomics . 10 (132): 132.
doi :
10.1186/1471-2164-10-132 .
PMC
2670323 .
PMID
19323823 .
^
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q Lee J, Cho CH, Park SI, Choi JW, Song HS, West JA, Bhattacharya D, Yoon HS (September 2016).
"Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants" . BMC Biology . 14 (1): 75.
doi :
10.1186/s12915-016-0299-5 .
PMC
5010701 .
PMID
27589960 .
^
a
b Janouškovec J, Liu SL, Martone PT, Carré W, Leblanc C, Collén J, Keeling PJ (2013-03-25). Bhattacharya D (ed.).
"Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers" . PLOS ONE . 8 (3): e59001.
Bibcode :
2013PLoSO...859001J .
doi :
10.1371/journal.pone.0059001 .
PMC
3607583 .
PMID
23536846 .
^ Ohta N, Matsuzaki M, Misumi O, Miyagishima SY, Nozaki H, Tanaka K, Shin-I T, Kohara Y, Kuroiwa T (April 2003).
"Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae" . DNA Research . 10 (2): 67–77.
doi :
10.1093/dnares/10.2.67 .
PMID
12755171 .
^ Glöckner G, Rosenthal A, Valentin K (October 2000). "The structure and gene repertoire of an ancient red algal plastid genome". Journal of Molecular Evolution . 51 (4): 382–90.
Bibcode :
2000JMolE..51..382G .
CiteSeerX
10.1.1.566.2529 .
doi :
10.1007/s002390010101 .
PMID
11040290 .
S2CID
23064129 .
^ Jain K, Krause K, Grewe F, Nelson GF, Weber AP, Christensen AC, Mower JP (December 2014).
"Extreme features of the Galdieria sulphuraria organellar genomes: a consequence of polyextremophily?" . Genome Biology and Evolution . 7 (1): 367–80.
doi :
10.1093/gbe/evu290 .
PMC
4316638 .
PMID
25552531 .
^
a
b
c
d Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS (March 2016).
"Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes" . Scientific Reports . 6 (1): 23744.
Bibcode :
2016NatSR...623744L .
doi :
10.1038/srep23744 .
PMC
4814812 .
PMID
27030297 .
^ Boo GH, Hughey JR (February 2019).
"Phylogenomics and multigene phylogenies decipher two new cryptic marine algae from California, Gelidium gabrielsonii and G. kathyanniae (Gelidiales, Rhodophyta)" . Journal of Phycology . 55 (1): 160–172.
doi :
10.1111/jpy.12802 .
PMID
30341779 .
^ Ho CL, Lee WK, Lim EL (March 2018).
"Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales)" . Genomics . 110 (2): 124–133.
doi :
10.1016/j.ygeno.2017.09.003 .
PMID
28890206 .
^ Campbell, Matthew A.; Presting, Gernot; Bennett, Matthew S.; Sherwood, Alison R. (2014-02-21). "Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta". Phycologia . 53 (2): 109–116.
doi :
10.2216/13-222.1 .
S2CID
85867132 .
^ Hagopian JC, Reis M, Kitajima JP, Bhattacharya D, de Oliveira MC (October 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.
Bibcode :
2004JMolE..59..464H .
CiteSeerX
10.1.1.614.9150 .
doi :
10.1007/s00239-004-2638-3 .
PMID
15638458 .
S2CID
19135480 .
^ DePriest MS, Bhattacharya D, López-Bautista JM (2013-07-19).
"The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae)" . PLOS ONE . 8 (7): e68246.
Bibcode :
2013PLoSO...868246D .
doi :
10.1371/journal.pone.0068246 .
PMC
3716797 .
PMID
23894297 .
^
a
b
c Cho CH, Choi JW, Lam DW, Kim KM, Yoon HS (2018-05-08).
"Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats" . PLOS ONE . 13 (5): e0196995.
Bibcode :
2018PLoSO..1396995C .
doi :
10.1371/journal.pone.0196995 .
PMC
5940233 .
PMID
29738547 .
^ Reith M, Munholland J (April 1993).
"A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea" . The Plant Cell . 5 (4): 465–475.
doi :
10.1105/tpc.5.4.465 .
PMC
160285 .
PMID
12271072 .
^ Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, et al. (August 2017).
"Porphyra umbilicalis (Bangiophyceae, Rhodophyta)" . Proceedings of the National Academy of Sciences of the United States of America . 114 (31): E6361–E6370.
doi :
10.1073/pnas.1703088114 .
PMC
5547612 .
PMID
28716924 .
^ Tajima N, Sato S, Maruyama F, Kurokawa K, Ohta H, Tabata S, Sekine K, Moriyama T, Sato N (May 2014). "Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum". Journal of Plant Research . 127 (3): 389–97.
doi :
10.1007/s10265-014-0627-1 .
PMID
24595640 .
S2CID
1420996 .
^
a
b
c Hughey JR, Gabrielson PW, Rohmer L, Tortolani J, Silva M, Miller KA, Young JD, Martell C, Ruediger E (June 2014).
"Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes" . Scientific Reports . 4 (1): 5113.
Bibcode :
2014NatSR...4E5113H .
doi :
10.1038/srep05113 .
PMC
4044621 .
PMID
24894641 .
^
a
b Wang L, Mao Y, Kong F, Li G, Ma F, Zhang B, Sun P, Bi G, Zhang F, Xue H, Cao M (2013-05-29).
"Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis" . PLOS ONE . 8 (5): e65902.
Bibcode :
2013PLoSO...865902W .
doi :
10.1371/journal.pone.0065902 .
PMC
3667073 .
PMID
23734264 .
^ Salomaki ED, Nickles KR, Lane CE (April 2015). "The ghost plastid of Choreocolax polysiphoniae". Journal of Phycology . 51 (2): 217–21.
doi :
10.1111/jpy.12283 .
PMID
26986516 .
S2CID
30670447 .
^ Löffelhardt W, Bohnert HJ, Bryant DA (1997). "The complete sequence of the Cyanophora paradoxa cyanelle genome (Glaucocystophyceae)". Plant Systematics and Evolution . Vol. 11. Springer Vienna. pp. 149–162.
doi :
10.1007/978-3-7091-6542-3_8 .
ISBN
9783211830352 .
^
a
b
c
d Kim JI, Moore CE, Archibald JM, Bhattacharya D, Yi G, Yoon HS, Shin W (July 2017).
"Evolutionary Dynamics of Cryptophyte Plastid Genomes" . Genome Biology and Evolution . 9 (7): 1859–1872.
doi :
10.1093/gbe/evx123 .
PMC
5534331 .
PMID
28854597 .
^ Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PS, Hara Y, Archibald JM (November 2009).
"The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate" . Genome Biology and Evolution . 1 : 439–48.
doi :
10.1093/gbe/evp047 .
PMC
2839278 .
PMID
20333213 .
^ Sánchez Puerta MV, Bachvaroff TR, Delwiche CF (2005-01-01).
"The complete plastid genome sequence of the haptophyte Emiliania huxleyi: a comparison to other plastid genomes" . DNA Research . 12 (2): 151–6.
doi :
10.1093/dnares/12.2.151 .
PMID
16303746 .
^ Douglas SE, Penny SL (February 1999). "The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae". Journal of Molecular Evolution . 48 (2): 236–44.
Bibcode :
1999JMolE..48..236D .
doi :
10.1007/PL00006462 .
PMID
9929392 .
S2CID
2005223 .
^ Cattolico RA, Jacobs MA, Zhou Y, Chang J, Duplessis M, Lybrand T, McKay J, Ong HC, Sims E, Rocap G (May 2008).
"Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains" . BMC Genomics . 9 (1): 211.
doi :
10.1186/1471-2164-9-211 .
PMC
2410131 .
PMID
18462506 .
^ Kowallik KV, Stoebe B, Schaffran I, Kroth-Pancic P, Freier U (December 1995). "The chloroplast genome of a chlorophylla+c-containing alga,Odontella sinensis". Plant Molecular Biology Reporter . 13 (4): 336–342.
doi :
10.1007/BF02669188 .
ISSN
0735-9640 .
S2CID
1515475 .
^
a
b Oudot-Le Secq MP, Grimwood J, Shapiro H, Armbrust EV, Bowler C, Green BR (April 2007). "Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage". Molecular Genetics and Genomics . 277 (4): 427–39.
doi :
10.1007/s00438-006-0199-4 .
PMID
17252281 .
S2CID
23192934 .
^ Khan H, Parks N, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM (August 2007).
"Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny" . Molecular Biology and Evolution . 24 (8): 1832–42.
doi :
10.1093/molbev/msm101 .
PMID
17522086 .
^ Kim JI, Yoon HS, Yi G, Kim HS, Yih W, Shin W (2015-06-05). Przyborski JM (ed.).
"The Plastid Genome of the Cryptomonad Teleaulax amphioxeia" . PLOS ONE . 10 (6): e0129284.
Bibcode :
2015PLoSO..1029284K .
doi :
10.1371/journal.pone.0129284 .
PMC
4457928 .
PMID
26047475 .
^ Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ (January 2007).
"The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts" . Molecular Biology and Evolution . 24 (1): 54–62.
doi :
10.1093/molbev/msl129 .
PMID
16990439 .
^
a
b
c Suzuki S, Hirakawa Y, Kofuji R, Sugita M, Ishida KI (July 2016). "Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species". Journal of Plant Research . 129 (4): 581–590.
doi :
10.1007/s10265-016-0804-5 .
PMID
26920842 .
S2CID
3463713 .
^ Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM (May 2014).
"Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae" . BMC Genomics . 15 (1): 374.
doi :
10.1186/1471-2164-15-374 .
PMC
4035089 .
PMID
24885563 .
^ Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A, Orsat B, Spielmann A, Stutz E (July 1993).
"Complete sequence of Euglena gracilis chloroplast DNA" . Nucleic Acids Research . 21 (15): 3537–44.
doi :
10.1093/nar/21.15.3537 .
PMC
331456 .
PMID
8346031 .
^ Cai X, Fuller AL, McDougald LR, Zhu G (December 2003). "Apicoplast genome of the coccidian Eimeria tenella". Gene . 321 : 39–46.
doi :
10.1016/j.gene.2003.08.008 .
PMID
14636990 .
^
a
b Suzuki S, Shirato S, Hirakawa Y, Ishida KI (2015).
"Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata" . Genome Biology and Evolution . 7 (6): 1533–1545.
doi :
10.1093/gbe/evv096 .
PMC
4494063 .
PMID
26002880 .
^ Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI (June 2006).
"Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus" . Proceedings of the National Academy of Sciences of the United States of America . 103 (25): 9566–71.
Bibcode :
2006PNAS..103.9566G .
doi :
10.1073/pnas.0600707103 .
PMC
1480447 .
PMID
16760254 .
^ Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, et al. (December 2012).
"Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs" (PDF) . Nature . 492 (7427): 59–65.
Bibcode :
2012Natur.492...59C .
doi :
10.1038/nature11681 .
PMID
23201678 .
^ Moore CE, Curtis B, Mills T, Tanifuji G, Archibald JM (2012).
"Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica CCMP1168 reveals lineage-specific gene loss and genome complexity" . Genome Biology and Evolution . 4 (11): 1162–75.
doi :
10.1093/gbe/evs090 .
PMC
3514955 .
PMID
23042551 .
^ Tanifuji G, Onodera NT, Wheeler TJ, Dlutek M, Donaher N, Archibald JM (2011).
"Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set" . Genome Biology and Evolution . 3 : 44–54.
doi :
10.1093/gbe/evq082 .
PMC
3017389 .
PMID
21147880 .
^ Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, Reith M, Cavalier-Smith T, Maier UG (April 2001).
"The highly reduced genome of an enslaved algal nucleus" . Nature . 410 (6832): 1091–6.
Bibcode :
2001Natur.410.1091D .
doi :
10.1038/35074092 .
PMID
11323671 .
^ Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM (December 2007).
"Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function" . Proceedings of the National Academy of Sciences of the United States of America . 104 (50): 19908–13.
Bibcode :
2007PNAS..10419908L .
doi :
10.1073/pnas.0707419104 .
PMC
2148396 .
PMID
18077423 .
^ Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM (May 2014).
"Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae" . BMC Genomics . 15 (1): 374.
doi :
10.1186/1471-2164-15-374 .
PMC
4035089 .
PMID
24885563 .
^ Nowack EC,
Melkonian M , Glöckner G (March 2008).
"Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes" . Current Biology . 18 (6): 410–8.
doi :
10.1016/j.cub.2008.02.051 .
PMID
18356055 .
External links
^ 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 .