User:DCDuring/List of sequenced plant genomes

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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 2012
Bathycoccus prasinos BBAN7 Green algae Comparative analysis 15 Mb Joint Genome Institute 2012
Chlamydomonas reinhardtii CC-503 cw92 mt+ Green algae Model organism 111 Mb 17,737 University of California at Los Angeles 2007 Template:NCBI taxid Template:ENA
Chlorella variabilis NC64A Green algae 2010
Coccomyxa subellipsoidea sp. C-169 Green algae Model biofuel Joint Genome Institute 2007
Dunaliella salina CCAP19/18 Green algae Halophilic, biofuel and beta-carotene production Joint Genome Institute Organelle genomes complete, nuclear genome in progress
Micromonas pusilla CCMP1545 Green algae Marine phytoplankton Joint Genome Institute 2007
Micromonas pusilla RCC299/NOUM17 Green algae Marine phytoplankton Joint Genome Institute 2007
Ostreococcus lucimarinus CCE9901 Green algae Simple eukaryote, small genome 13.2 Mb 7,796 2007
Ostreococcus tauri OTH95 Green algae Simple eukaryote, small genome 2006
Ostreococcus sp. RCC809 Green algae 7,773 Joint Genome Institute 2008
Volvox carteri Green algae Multicellular alga, model organism ~131.2 Mb 14,971 2010
Chondrus crispus Red algae 105 Mb 9,606 Genoscope/Station Biologique de Roscoff 2013
Cyanidioschyzon merolae Strain:10D Red algae Photo-autotrophic 16.73 Mb 5,017 2004, 2007
Galdieria sulphuraria Red algae Thermo-acidophilic (extremophile) 13.7 Mb 6,623 2005 2005 2013
Porphyridium purpureum Red algae 19.7 Mb 8,355 2013
Pyropia yezoensis Red algae 43 Mb 10,327 2013
Ectocarpus siliculosus Brown algae (Heterokontophyta) distantly related to plants Station Biologique de Roscoff 2010

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

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

Angiosperms

Amborellales - amborellales#English - amborellales#Latin - Special:WhatLinksHere/Amborellales - Amborellales@WSp - Amborellales@WP - Google Amborellales (Books • Groups • Scholar) - Amborellales at List of Prokaryotic names with Standing in Nomenclature - Fossilworks

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

Eudicots

Ranunculales
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Aquilegia coerulea Ranunculaceae Basal eudicot Unpublished
Proteales
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Nelumbo nucifera Nelumbonaceae Basal eudicot 2013
Caryophyllales
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Beta vulgaris (sugar beet) Amaranthaceae
(formerly Chenopodiaceae)		 Crop plant 714–758 Mbp 27,421 2013
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
Aethionema arabicum Brassicaceae Comparative analysis of crucifer genomes 2013
Arabidopsis lyrata Brassicaceae model plant 2011
Arabidopsis thaliana Ecotype:Columbia Brassicaceae Model plant 135 Mbp 2000
Brassica rapa (Chinese cabbage) Brassicaceae Assorted crops and model organism 2011
Capsella rubella Brassicaceae Close relative of Arabidopsis thaliana 130Mbp 26,521 JGI 2013? 2013
Eutrema salsugineum Brassicaceae A relative of arabidopsis with high salt tolerance 240Mbp 26,351 JGI 2013
Eutrema parvulum Brassicaceae Comparative analysis of crucifer genomes 2013
Leavenworthia alabamica Brassicaceae Comparative analysis of crucifer genomes 2013
Sisymbrium irio Brassicaceae Comparative analysis of crucifer genomes 2013
Thellungiella parvula Brassicaceae A relative of arabidopsis with high salt tolerance 2011
Cannabis sativa (hemp) Cannabaceae Hemp and marijuana production ca 820Mbp 30,074 based on transcriptome assembly and clustering 2011 Illumina/454

scaffold N50 16.2 Kbp

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

scaffold N50

1Mbp

total coverage ~3x (Sanger)

92.1% unigenes mapped

235Mbp anchored (of this 161Mbp also oriented)

Kalanchoe Crassulaceae 2013?
Citrullus lanatus (watermelon) Cucurbitaceae Tasty ca 425Mbp 23,440 BGI 2012 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 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 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
Jatropha curcas Palawan Euphorbiaceae bio-diesel crop 2010
Manihot esculenta (Cassava) Euphorbiaceae Humanitarian importance ~760Mb 30,666 JGI 2012
Ricinus communis (Castor bean) Euphorbiaceae Oilseed crop 320Mbp 31,237 JCVI 2010 Sanger coverage~4.6x contig N50 21.1 kbp scaffold N50 496.5kbp
Cajanus cajan (Pigeon pea) var. Asha Fabaceae Model legume 2012
Cicer arietinum (chickpea) Fabaceae filling 2013
Cicer arietinum L. (chickpea) Fabaceae 2013
Glycine max (soybean) var. Williams 82 Fabaceae Protein and oil crop 1115Mbp 46,430 2010 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
Medicago truncatula (Barrel Medic) Fabaceae Model legume 2011
Phaseolus vulgaris (common bean) Fabaceae Model bean 520Mbp 31,638 JGI 2013?
Linum usitatissimum (flax) Linaceae Crop ~350Mbp 43,384 BGI et al. 2012
Gossypium raimondii Malvaceae One of the putative progenitor species of tetraploid cotton 2013?
Theobroma cacao (cocoa tree) Malvaceae Flavouring crop 2010
Theobroma cacao (cocoa tree) cv. Matina 1-6 Malvaceae Most widely cultivated cacao type 2013
Azadirachta indica (neem) Meliaceae Source of number of Terpenoids, including biopesticide azadirachtin, Used in Traditional Medicine 364 Mbp ~20000 GANIT Labs 2012 and 2011 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
Fragaria vesca (wild strawberry) Rosaceae Fruit crop 240Mbp 34,809 2011 scaffold N50: 1.3 Mbp

454/Illumina/solid

39x coverage

WGS

Malus domestica (apple) "Golden Delicious" Rosaceae Fruit crop ~742.3Mbp 57,386 2010 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?
Prunus avium (sweet cherry) cv. Stella Rosaceae Fruit crop 2013?
Prunus mume (Chinese plum or Japanese apricot) Rosaceae Fruit crop 2012
Prunus persica (peach) Rosaceae Fruit crop 265Mbp 27,852 2013 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
Pyrus communis (European pear) cv. Doyenne du Comice Rosaceae Fruit crop 2013?
Citrus clementina (Clementine) Rutaceae Fruit crop 2013?
Citrus sinensis (Sweet orange) Rutaceae Fruit crop 2013?, 2013
Populus trichocarpa (poplar) Salicaceae Carbon sequestration, model tree, timber 510 Mbp (cytogenetic) 485 Mbp (coverage) 73,013 2006 Scaffold N50: 19.5 Mbp

Contig N50:552.8 Kbp

WGS

>=95 % cDNA found

Vitis vinifera (grape) genotype PN40024 Vitaceae fruit crop 2007
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? 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 2012 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 Illumina

contig N50: 5100bp

~40x coverage

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

79.2x coverage

contig N50: 31,429bp

scaffold N50: 1,318,511bp

Nicotiana benthamiana Solanaceae Close relative of tobacco ca 3Gbp 2012 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 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 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

(b) 2014

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 N50 contig: 52.2 kb

N50 scaffold: 0.45 Mb

Petunia Solanaceae Economically important flower 2011
Utricularia gibba (humped bladderwort) Lentibulariaceae model system for studying genome size evolution; a carnivorous plant 81.87 Mb 28,494 LANGEBIO, CINVESTAV 2013 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
Aegilops tauschii (Tausch's goatgrass) Poaceae bread wheat D-genome progenitor ca 4.36Gb BGI 2013 Non-repetitive sequence assembled
Brachypodium distachyon (purple false brome) Poaceae Model monocot 2010
Hordeum vulgare (barley) Poaceae Model of ecological adoption IBSC 2012
Oryza brachyantha (wild rice) Poaceae Disease resistant wild relative of rice 2013
Oryza glaberrima (African rice) var CG14 Poaceae West-African species of rice 2010
Oryza sativa (short grain rice) ssp indica Poaceae Crop and model cereal 2002
Oryza sativa (long grain rice) ssp japonica Poaceae Crop and model cereal 2002
Panicum virgatum (switchgrass) Poaceae biofuel 2013?
Phyllostachys edulis (moso bamboo) Poaceae 2013
Sorghum bicolor genotype BTx623 Poaceae Crop ca 730Mbp 34,496 2009 contig N50:195.4kbp

scaffold N50: 62.4Mbp

Sanger, 8.5x coverage

WGS

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

Roche 454/Illumina WGS

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

Illumina WGS

Zea mays ssp mays B73 Poaceae Cereal crop 2,300Mbp 39,656 2009 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 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 N50 contig: 7.9 kb
Phoenix dactylifera (Date palm) Arecaceae Woody crop in arid regions 658 Mbp 28,800 2011 N50 contig: 6.4 kb
Elaeis guineensis (African oil palm) Arecaceae Oil-bearing crop ~1800 Mbp 34,800 2013 N50 scaffold: 1.27 Mb
Spirodela polyrhiza (Greater duckweed) Araceae Aquatic plant 158 Mbp 19,623 2014 N50 scaffold: 3.76 Mb

Gymnosperms

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
Picea glauca (White spruce) Pinaceae Timber, Pulp 20.8 Gb 56,064 Institutional Collaboration 2013
Pinus taeda (Loblolly pine) Pinaceae Timber 20.15 Gb 50,172 Institutional collaboration 2014 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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