List of sequenced plant genomes

This list of sequenced plant genomes contains plant species known to have publicly available complete genome sequences that have been assembled, annotated and published. Unassembled genomes are not included, nor are organelle only sequences. For all kingdoms, see the list of sequenced genomes.

Algae

Unicellular photosynthetic eukaryotes.

Organism strain Clade Relevance Genome size Number of genes predicted Organization Year of completion Assembly status Links
Cyanophora paradoxa Glaucophyte Rutgers University[1] 2012[1]
Bathycoccus prasinos BBAN7 Green algae Comparative analysis 15 Mb Joint Genome Institute 2012[2]
Chlamydomonas reinhardtii CC-503 cw92 mt+ Green algae Model organism 111 Mb 17,737 University of California at Los Angeles[3] 2007 "Chlamydomonas reinhardtii". National Center for Biotechnology Information (NCBI).  ENA GCA_000002595
Chlorella variabilis NC64A Green algae 2010[4]
Coccomyxa subellipsoidea sp. C-169 Green algae Model biofuel Joint Genome Institute 2007[5]
Dunaliella salina CCAP19/18 Green algae Halophilic, biofuel and beta-carotene production Joint Genome Institute Organelle genomes complete,[6] nuclear genome in progress
Micromonas pusilla CCMP1545 Green algae Marine phytoplankton Joint Genome Institute 2007[7][8]
Micromonas pusilla RCC299/NOUM17 Green algae Marine phytoplankton Joint Genome Institute 2007[8][9]
Ostreococcus lucimarinus CCE9901 Green algae Simple eukaryote, small genome 13.2 Mb 7,796 2007[10]
Ostreococcus tauri OTH95 Green algae Simple eukaryote, small genome 2006[11]
Ostreococcus sp. RCC809 Green algae 7,773 Joint Genome Institute 2008[12]
Volvox carteri Green algae Multicellular alga, model organism ~131.2 Mb 14,971 2010[13]
Chondrus crispus Red algae 105 Mb 9,606 Genoscope/Station Biologique de Roscoff 2013[14]
Cyanidioschyzon merolae Strain:10D Red algae Photo-autotrophic 16.73 Mb5,017 2004,[15] 2007 [16]
Galdieria sulphuraria Red algae Thermo-acidophilic (extremophile) 13.7 Mb6,623 2005[17] 2005 [18] 2013 [19]
Porphyridium purpureum Red algae 19.7 Mb8,355 2013 [20]
Pyropia yezoensis Red algae 43 Mb10,327 2013 [21]
Ectocarpus siliculosus Brown algae (Heterokontophyta) distantly related to plants Station Biologique de Roscoff 2010[22]

Bryophytes

Organism strain Division Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Physcomitrella patens ssp. patens str. Gransden 2004 Bryophytes Early diverging land plant 2008[23]

Higher plants (vascular plants)

Organism strain Division Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Selaginella moellendorffii Lycopodiophyta Model organism 2011[24][25]

Angiosperms

Amborellales

Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Amborella trichopoda Amborellaceae Basal angiosperm 2013[26][27]

Eudicots

Ranunculales
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Aquilegia caerulea Ranunculaceae Basal eudicot Unpublished[28]
Proteales
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Nelumbo nucifera Nelumbonaceae Basal eudicot 2013[29]
Caryophyllales
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Beta vulgaris (sugar beet) Chenopodiaceae Crop plant 714–758 Mbp 27,421 2013[30]
Rosids
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Betula nana (dwarf birch) Betulaceae Arctic shrub 450 Mbp QMUL/SBCS 2013[31]
Aethionema arabicum Brassicaceae Comparative analysis of crucifer genomes 2013[32]
Arabidopsis lyrata Brassicaceae model plant 2011[33]
Arabidopsis thaliana Ecotype:Columbia Brassicaceae Model plant 135 Mbp 2000[34]
Brassica rapa (Chinese cabbage) Brassicaceae Assorted crops and model organism 2011[35]
Capsella rubella Brassicaceae Close relative of Arabidopsis thaliana 130Mbp 26,521 JGI 2013?[36] 2013[37]
Eutrema salsugineum Brassicaceae A relative of arabidopsis with high salt tolerance 240Mbp 26,351 JGI 2013[38]
Eutrema parvulum Brassicaceae Comparative analysis of crucifer genomes 2013[32]
Leavenworthia alabamica Brassicaceae Comparative analysis of crucifer genomes 2013[32]
Sisymbrium irio Brassicaceae Comparative analysis of crucifer genomes 2013[32]
Thellungiella parvula Brassicaceae A relative of arabidopsis with high salt tolerance 2011[39]
Cannabis sativa (hemp) Cannabaceae Hemp and marijuana production ca 820Mbp 30,074 based on transcriptome assembly and clustering 2011[40] Illumina/454

scaffold N50 16.2 Kbp

Carica papaya (papaya) Caricaceae Fruit crop 372Mbp 28,629 2008[41] contig N50 11kbp

scaffold N50

1Mbp

total coverage ~3x (Sanger)

92.1% unigenes mapped

235Mbp anchored (of this 161Mbp also oriented)

Kalanchoe Crassulaceae 2013?[42]
Citrullus lanatus (watermelon) Cucurbitaceae Vegetable crop ca 425Mbp 23,440 BGI 2012[43] Illumina

coverage 108.6x

contig N50 26.38 kbp

Scaffold N50 2.38 Mbp

genome covered 83.2%

~97% ESTs mapped

Cucumis melo (Muskmelon) DHL92 Cucurbitaceae Vegetable crop 450Mbp 27,427 2012[44] 454

13.5x coverage

contig N50: 18.1kbp

scaffold N50: 4.677 Mbp

WGS

Cucumis sativus (cucumber) 'Chinese long' inbred line 9930 Cucurbitaceae Vegetable crop 350 Mbp (Kmer depth) 367 Mbp (flow cytometry) 26,682 2009[45] contig N50 19.8kbp

scaffold N50 1,140kbp

total coverage ~72.2 (Sanger + Ilumina)

96.8% unigenes mapped

72.8% of the genome anchored

Hevea brasiliensis (rubber tree) Euphorbiaceae the most economically important member of the genus Hevea 2013[46]
Jatropha curcas Palawan Euphorbiaceae bio-diesel crop 2010[47]
Manihot esculenta (Cassava) Euphorbiaceae Humanitarian importance ~760Mb 30,666 JGI 2012[48]
Ricinus communis (Castor bean) Euphorbiaceae Oilseed crop 320Mbp 31,237 JCVI 2010[49] Sanger coverage~4.6x contig N50 21.1 kbp scaffold N50 496.5kbp
Cajanus cajan (Pigeon pea) var. Asha Fabaceae Model legume 2012[50][51]
Arachis duranensis (A genome diploid wild peanut) accession V14167 Fabaceae Wild ancestor of peanut, an oilseed and grain legume crop 2016[52] Illumina 154x coverage, contig N50 22 kbp, scaffold N50 948 kbp
Arachis ipaensis (B genome diploid wild peanut) accession K30076 Fabaceae Wild ancestor of peanut, an oilseed and grain legume crop 2016[52] Illumina 163x coverage, contig N50 23 kbp, scaffold N50 5,343 kbp
Cicer arietinum (chickpea) Fabaceae filling 2013[53]
Cicer arietinum L. (chickpea) Fabaceae 2013[54]
Glycine max (soybean) var. Williams 82 Fabaceae Protein and oil crop 1115Mbp 46,430 2010[55] Contig N50:189.4kbp

Scaffold N50:47.8Mbp

Sanger coverage ~8x

WGS

955.1 Mbp assembled

Lotus japonicus (Bird's-foot Trefoil) Fabaceae Model legume 2008[56]
Medicago truncatula (Barrel Medic) Fabaceae Model legume 2011[57]
Phaseolus vulgaris (common bean) Fabaceae Model bean 520Mbp 31,638 JGI 2013?[58]
Linum usitatissimum (flax) Linaceae Crop ~350Mbp 43,384 BGI et al. 2012 [59]
Gossypium raimondii Malvaceae One of the putative progenitor species of tetraploid cotton 2013?[60]
Theobroma cacao (cocoa tree) Malvaceae Flavouring crop 2010[61][62]
Theobroma cacao (cocoa tree) cv. Matina 1-6 Malvaceae Most widely cultivated cacao type 2013[63]
Azadirachta indica (neem) Meliaceae Source of number of Terpenoids, including biopesticide azadirachtin, Used in Traditional Medicine 364 Mbp ~20000 GANIT Labs 2012[64] and 2011[65] Illumina GAIIx, scaffold N50 of 452028bp, Transcriptome data from Shoot, Root, Leaf, Flower and Seed
Eucalyptus grandis (Rose gum) Myrtaceae Fibre and timber crop 2011[66]
Fragaria vesca (wild strawberry) Rosaceae Fruit crop 240Mbp 34,809 2011[67] scaffold N50: 1.3 Mbp

454/Illumina/solid

39x coverage

WGS

Malus domestica (apple) "Golden Delicious" Rosaceae Fruit crop ~742.3Mbp 57,386 2010[68] contig N50 13.4 (kbp??)

scafold N50 1,542.7 (kbp??)

total coverage ~16.9x (Sanger + 454)

71.2% anchored

Prunus amygdalus (almond) Rosaceae Fruit crop 2013?[69]
Prunus avium (sweet cherry) cv. Stella Rosaceae Fruit crop 2013?[69]
Prunus mume (Chinese plum or Japanese apricot) Rosaceae Fruit crop 2012[70]
Prunus persica (peach) Rosaceae Fruit crop 265Mbp 27,852 2013[71] Sanger coverage:8.47x

WGS

ca 99% ESTs mapped

215.9 Mbp in pseudomolecules

Pyrus bretschneideri (ya pear or Chinese white pear) cv. Dangshansuli Rosaceae Fruit crop 2012[72]
Pyrus communis (European pear) cv. Doyenne du Comice Rosaceae Fruit crop 2013?[69]
Citrus clementina (Clementine) Rutaceae Fruit crop 2013?[73]
Citrus sinensis (Sweet orange) Rutaceae Fruit crop 2013?,[73] 2013[74]
Populus trichocarpa (poplar) Salicaceae Carbon sequestration, model tree, timber 510 Mbp (cytogenetic) 485 Mbp (coverage) 73,013 [Phytozome] 2006[75] Scaffold N50: 19.5 Mbp

Contig N50:552.8 Kbp [phytozome]

WGS

>=95 % cDNA found

Vitis vinifera (grape) genotype PN40024 Vitaceae fruit crop 2007[76]
Asterids
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Mimulus guttatus Scrophulariaceae model system for studying ecological and evolutionary genetics ca 430Mbp 26,718 JGI 2013?[77] Scaffold N50 = 1.1 Mbp

Contig N50 = 45.5 Kbp

Solanum lycopersicum (tomato) cv. Heinz 1706 Solanaceae Food crop ca 900Mbp 34,727 SGN 2011[78] 2012[79] Sanger/454/Illumina/Solid

Pseudomolecules spanning 91 scaffolds (760Mbp of which 594Mbp have been oriented )

over 98% ESTs mappable

Solanum pimpinellifolium (Currant Tomato) Solanaceae closest wild relative to tomato 2012[79] Illumina

contig N50: 5100bp

~40x coverage

Solanum tuberosum (potato) Solanaceae Food crop 844 Mbp kmer (856 Mbp) 39,031 PGSC 2011[80] Sanger/454/Illumina

79.2x coverage

contig N50: 31,429bp

scaffold N50: 1,318,511bp

Solanum commersonii (commerson's nightshade) Solanaceae Wild potato relative 838 Mbp kmer (840 Mbp) 37,662 UNINA, UMN, UNIVR, Sequentia Biotech, CGR 2015[81] Illumina

105x coverage

contig N50: 6,506bp

scaffold N50: 44,298bp

Nicotiana benthamiana Solanaceae Close relative of tobacco ca 3Gbp 2012[82] Illumina

63x coverage

contig N50: 16,480bp

scaffold N50:89,778bp

>93% unigenes found

Nicotiana sylvestris (Tobacco plant) Solanaceae model system for studies of terpenoid production 2.636Gbp Philip Morris International 2013[83] 94x coverage

scaffold N50: 79.7 kbp

194kbp superscaffolds using physical Nicotiana map

Nicotiana tomentosiformis Solanaceae Tobacco progenitor 2.682 Gb Philip Morris International 2013[83] 146x coverage

scaffold N50: 82.6 kb

166kbp superscaffolds using physical Nicotiana map

Capsicum annuum (Pepper)

(a) cv. CM334 (b) cv. Zunla-1

 Solanaceae Food crop ~3.48 Gbp (a) 34,903

(b) 35,336

 (a) 2014[84]

(b) 2014[85]

 N50 contig: (a) 30.0 kb (b) 55.4 kb

N50 scaffold: (a) 2.47 Mb (b) 1.23 Mb

Capsicum annuum var. glabriusculum (Chiltepin) Solanaceae Progenitor of cultivated pepper ~3.48 Gbp 34,476 2014[85] N50 contig: 52.2 kb

N50 scaffold: 0.45 Mb

Petunia Solanaceae Economically important flower 2011[86]
Utricularia gibba (humped bladderwort) Lentibulariaceae model system for studying genome size evolution; a carnivorous plant 81.87 Mb 28,494 LANGEBIO, CINVESTAV 2013[87] Scaffold N50: 80.839 Kb

Monocots

Grasses
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Setaria italica (Foxtail millet) Poaceae Model of C4 metabolism 2012[88]
Aegilops tauschii (Tausch's goatgrass) Poaceae bread wheat D-genome progenitor ca 4.36Gb BGI 2013[89] Non-repetitive sequence assembled
Brachypodium distachyon (purple false brome) Poaceae Model monocot 2010[90]
Hordeum vulgare (barley) Poaceae Model of ecological adoption IBSC 2012[91]
Oryza brachyantha (wild rice) Poaceae Disease resistant wild relative of rice 2013[92]
Oryza glaberrima (African rice) var CG14 Poaceae West-African species of rice 2010[93]
Oryza rufipogon (red rice) Poaceae Ancestor to Oryza sativa 406 Mb 37,071 SIBS 2012 [94] Illumina HiSeq2000

100x coverage

Oryza sativa (short grain rice) ssp indica Poaceae Crop and model cereal 2002[95]
Oryza sativa (long grain rice) ssp japonica Poaceae Crop and model cereal 2002[96]
Panicum virgatum (switchgrass) Poaceae biofuel 2013?[97]
Phyllostachys edulis (moso bamboo) Poaceae 2013[98]
Sorghum bicolor genotype BTx623 Poaceae Crop ca 730Mbp 34,496 2009[99] contig N50:195.4kbp

scaffold N50: 62.4Mbp

Sanger, 8.5x coverage

WGS

Triticum aestivum (bread wheat) Poaceae 20% of global nutrition 2012[100] Non-repetitive sequence assembled

Roche 454/Illumina WGS

Triticum urartu Poaceae Bread wheat A-genome progenitor ca 4.94Gb BGI 2013[101] Non-repetitive sequence assembled

Illumina WGS

Zea mays (maize) ssp mays B73 Poaceae Cereal crop 2,300Mbp 39,656[102] 2009[103] contig N50 40kbp

scaffold N50: 76kbp

Sanger, 4-6x coverage per BAC

Other non-grasses
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Musa acuminata (Banana) Musaceae A-genome of modern banana cultivars 523 Mbp 36,542 2012[104] N50 contig: 43.1 kb

N50 scaffold: 1.3 Mb

Musa balbisiana (Wild banana) Musaceae B-genome of modern banana cultivars 438 Mbp 36,638 2013[105] N50 contig: 7.9 kb
Phoenix dactylifera (Date palm) Arecaceae Woody crop in arid regions 658 Mbp 28,800 2011[106] N50 contig: 6.4 kb
Elaeis guineensis (African oil palm) Arecaceae Oil-bearing crop ~1800 Mbp 34,800 2013[107] N50 scaffold: 1.27 Mb
Spirodela polyrhiza (Greater duckweed) Araceae Aquatic plant 158 Mbp 19,623 2014[108] N50 scaffold: 3.76 Mb

Gymnosperm

Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Picea abies (Norway spruce) Pinaceae Timber, tonewood, ornamental such as Christmas tree 20 Gb 28,354 Umeå Plant Science Centre / SciLifeLab, Sweden 2013[109]
Picea glauca (White spruce) Pinaceae Timber, Pulp 20.8 Gb 56,064 Institutional Collaboration 2013[110]
Pinus taeda (Loblolly pine) Pinaceae Timber 20.15 Gb50,172 Institutional collaboration 2014[111][112][113] N50 scaffold size: 66.9 kbp

Uncategorised things to add...

the genome from Galdieria sulphuraria has finally been published (Schönknecht, G., W.-H. Chen, et al. (2013). "Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote." Science 339(6124): 1207-1210.) Genome size is 13.7 MB, and 6623 protein-coding genes were annotated.

Nakamura et al. published the genome sequence for Pyropia yezoensis (Nakamura, Y., N. Sasaki, et al. (2013). "The first symbiont-free genome sequence of marine red alga, Susabi-nori Pyropia yezoensis." PLoS ONE 8(3): e57122.).

Bhattacharya et al. published the genome of Porphyridium purpureum (Bhattacharya, D., D. C. Price, et al. (2013). "Genome of the red alga Porphyridium purpureum." Nature Communications 4.)

Press releases announcing sequencing

Not meeting criteria of the first paragraph of this article in being nearly full sequences with high quality, published, assembled and publicly available. This list includes species where sequences are announced in press releases or websites, but not in a data-rich publication in a refereed Journal with doi.

See also

References

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  2. ↑ Genome Biology | Full text | Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
  3. ↑ Merchant; Prochnik, SE; Vallon, O; Harris, EH; Karpowicz, SJ; Witman, GB; Terry, A; Salamov, A; et al. (2007). "The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions". Science. 318 (5848): 245–250. Bibcode:2007Sci...318..245M. doi:10.1126/science.1143609. PMC 2875087Freely accessible. PMID 17932292.
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  5. ↑ Coccomyxa JGI entry
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  17. ↑ Galdieria sulphuraria Genome Project at MSU
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  42. ↑ Kalanchoe
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  44. ↑ The genome of melon (Cucumis melo L.)
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