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List of sequenced plant genomes

From Wikipedia, the free encyclopedia

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.

See also List of sequenced algae genomes.

Bryophytes

[edit]
Organism strain Division Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Anthoceros angustus Bryophytes Early diverging land plant
Ceratodon purpureus Bryophytes Early diverging land plant
Fontinalis antipyretica (greater water-moss) Bryophytes Aquatic moss 385.2 Mbp 16,538 BGI 2020[1] BGISEQ-500 & 10X, scaffold N50 45.8 Kbp
Marchantia polymorpha Bryophytes Early diverging land plant 225.8 Mb 19,138 2017[2]
Physcomitrella patens ssp. patens str. Gransden 2004 Bryophytes Early diverging land plant 462.3 Mbp 35,938 2008[3]
Pleurozium schreberi (feather moss) Bryophytes Ubiquitous moss species 318 Mbp 15,992 2019[4]

Vascular plants

[edit]

Lycophytes

[edit]
Organism strain Division Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Isoetes sinensis Lycopodiophyta First aquatic Quillwort 2.131 GB 57,303 2023[5] Scaffold N50 = 86 Mb
Selaginella moellendorffii Lycopodiophyta Model organism 106 Mb 22,285 2011[6][7] scaffold N50 = 1.7 Mb
Selaginella lepidophylla Lycopodiophyta Desiccation tolerance 122 Mb 27,204 2018[8] contig N50 = 163 kb

Ferns

[edit]
Organism strain Division Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Azolla filiculoides Polypodiophyta Fern 0.75 Gb 20,201 2018[9]
Salvinia cucullata Polypodiophyta Fern 0.26 Gb 19,914 2018[9]
Ceratopteris richardii Polypodiophyta Model organism 7.5 Gb 36,857 2019 (v1.1),[10] 2021 (v2.1)[11] Partial assembly consisting of 7.5 Gb/11.2 Gb, arranged in 39 chromosomes
Alsophila spinulosa Polypodiophyta Tree Fern 6.23 Gb 67,831 2022[12]

Gymnosperms

[edit]
Organism strain Division Relevance Genome size Number of genes predicted No of chromosomes Organization Year of completion Assembly status
Cycas panzhihuaensis (Dukou sago palm) Cycadophyta Rare and vulnerable species of cycad 10.5 Gb 2022[13]
Picea abies (Norway spruce) Pinales Timber, tonewood, ornamental such as Christmas tree 19.6 Gb 26,359[14] 12 Umeå Plant Science Centre / SciLifeLab, Sweden 2013[15]
Picea glauca (White spruce) Pinales Timber, Pulp 20.8 Gb 14,462[14] 12 Institutional Collaboration 2013[16][17]
Pinus taeda (Loblolly pine) Pinales Timber 20.15 Gb 9,024[14] 12 2014[18][19][20] N50 scaffold size: 66.9 kbp
Pinus lambertiana (Sugar pine) Pinales Timber; with the largest genomes among the pines;

the largest pine species

31 Gb 13,936 12 2016[14] 61.5X sequence coverage, platforms used:

Hiseq 2000, Hiseq 2500, GAIIx, MiSeq

Ginkgo biloba Ginkgoales 11.75 Gb 41,840 2016[21] N50 scaffold size: 48.2 kbp
Pseudotsuga menziesii Pinales 16 Gb 54,830 13 2017[22] N50 scaffold size : 340.7 kbp
Gnetum monatum Gnetales 4.07 Gb 27,491 2018[23]
Larix sibirica Pinales 12.34 Gbp 2019[24] scaffold N50 of 6440 bp
Abies alba Pinales 18.16 Gb 94,205 2019[25] scaffold N50 of 14,051 bp

Angiosperms

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Amborellales

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

Chlorantales

[edit]
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Chloranthus spicatus (Thunb.) Makino,[28] (Pearl Orchid) Chlorantaceae 2021[29] saffold N50 of 191.37 Mb

Magnoliales

Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Annona muricata Annonaceae Commercially grown fruit, medicinal applications 799.11 Mb 23,375 Institute for Biodiversity and Environmental Research (UBD)

Alliance for Conservation Tree Genomics

Biodiversity Genomics Team

2021[30] PacBio and Illumina short‐reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo‐chromosomes using Hi‐C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb).
Salix arbutifolia
(syn. Chosenia arbutifolia) 		Salicaceae Seriously endangered relic species 338.93 Mb 33,229 2022[31] Contig N50 of 1.68 Mb
Cinnamomum kanehirae (Stout camphor tree) Lauraceae 730.7 Mb 2019[32]

Eudicots

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Proteales
[edit]
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Macadamia integrifolia HAES 741 (Macadamia nut) Proteaceae Commercially grown nut 745 Mb 34,274 2020[33] N50 413 kb
Macadamia jansenii Proteaceae Rare relative of macademia nut 750 Mbp 2020[34] Compared Nanopore, Illumina and BGI stLRF data
Nelumbo nucifera (sacred lotus) Nelumbonaceae Basal eudicot 929 Mbp 2013[35] contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp
Ranunculales
[edit]
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Aquilegia coerulea Ranunculaceae Basal eudicot Unpublished[36]
Trochodendrales
[edit]
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Trochodendron aralioides (Wheel tree) Trochodendrales Basal eudicot having secondary xylem without vessel elements 1.614 Gb 35,328 Guangxi University 2019[37] 19 scaffolds corresponding to 19 chromosomes
Caryophyllales
[edit]
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[38]
Chenopodium quinoa Chenopodiaceae Crop plant 1.39–1.50 Gb 44,776 2017[39] 3,486 scaffolds, scaffold N50 of 3.84 Mb, 90% of the assembled genome is contained in 439 scaffolds[39]
Amaranthus hypocondriacus Amaranthaceae Crop plant 403.9 Mb 23,847 2016[40] 16 large scaffolds from 16.9 to 38.1 Mb. N50 and L50 of the assembly was 24.4 Mb and 7, respectively.[41]
Carnegiea gigantea Cactaceae Wild plant 1.40 Gb 28,292 2017[42] 57,409 scaffolds, scaffold N50 of 61.5 kb[42]
Nepenthes mirabilis Nepenthes Carnivorous Plant 691 Mb 42,961 2023[43] 159,555 contigs/scaffolds and N50 of 10,307 bp
Suaeda aralocaspica Amaranthaceae Performs complete C4 photosynthesis within individual cells (SCC4) 467 Mb 29,604 ABLife Inc. 2019[44] 4,033 scaffolds, scaffold N50 length of 1.83 Mb
Simmondsia chinensis (jojoba) Simmondsiaceae Oilseed Crop 887 Mb 23,490 2020[45] 994 scaffolds, scaffold N50 length of 5.2 Mb

Drosera capensis

Droseraceae Carnivorous Plant 263.79 Mb 2016[46] 12,713 scaffolds[46]
Tamarix chinensis (Chinese tamarisk) Tamaricaceae Margin tree 1.32 Gb 2023[47]
Rosids
[edit]
Organism strain Family Relevance Genome size Number of genes predicted No of chromosomes Organization Year of completion Assembly status
Bretschneidera sinensis Akaniaceae endangered relic tree species 1.21 Gb 45,839 2022[48]
Sclerocarya birrea

(Marula)

Anacardiaceae Used for food 18,397 2018[49][50]
Begonia masoniana (Iron cross begonia) Begoniaceae Flower 799.83 Mb 2022[51]
Begonia peltatifolia (Rex begonia) Begoniaceae Flower 331.75 Mb 2022[51]
Betula pendula (silver birch) Betulaceae Boreal forest tree, model for forest biotechnology 435 Mbp[52] 28,399 14 University of Helsinki 2017[52] 454/Illumina/PacBio. Assembly size 435 Mbp. Contig N50: 48,209 bp, scaffold N50: 239,796 bp. 89% of the assembly mapped to 14 pseudomolecules. Additionally 150 birch individuals sequenced.
Betula platyphylla (Japanese white birch) Betulaceae Pioneer hardwood tree species 430 Mbp 2021[53] contig N50 = 751 kbp
Betula nana (dwarf birch) Betulaceae Arctic shrub 450 Mbp QMUL/SBCS 2013[54]
Corylus heterophylla Fisch (Asian hazel) Betulaceae Nut tree used for food 370.75 Mbp 27,591 11 2021[55] Nanopore/Hi-C chromosome scale. Contig N50 and scaffold N50 sizes of 2.07 and 31.33  Mb, respectively
Corylus mandshurica Betulaceae Hazel used for breeding 367.67 Mb 28,409 11 2021[56]
Aethionema arabicum Brassicaceae Comparative analysis of crucifer genomes 2013[57]
Arabidopsis lyrata ssp. lyrata strain MN47 Brassicaceae Model plant 206.7 Mbp 32,670[58] 8 2011[58] 8.3X sequence coverage, analyzed on ABI 3730XL capillary sequencers
Arabidopsis thaliana Ecotype:Columbia Brassicaceae Model plant 135 Mbp 27,655[59] 5 AGI 2000[60]
Barbarea vulgaris

G-type

Brassicaceae Model plant for specialised metabolites and plant defenses 167.7 Mbp 25,350 8 2017[61] 66.5 X coverage with Illumina GA II technology
Brassica rapa ssp. pekinensis (Chinese cabbage) accession Chiifu-401-42 Brassicaceae Assorted crops and model organism 485 Mbp 41,174 (has undergone genome triplication) 10 The Brassica rapa Genome Sequencing Project Consortium 2011[62] 72X coverage of paired short read sequences generated by Illumina GA II technology
Brassica napus (Oilseed rape or rapeseed) European winter oilseed cultivar 'Darmor-bzh' Brassicaceae Crops 1130 Mbp 101,040 19 Institutional Collaboration 2014[63] 454 GS-FLX+ Titanium (Roche, Basel, Switzerland) and Sanger sequencing. Correction and gap filling used 79 Gb of Illumina (San Diego, CA) HiSeq sequence.
Capsella rubella Brassicaceae Close relative of Arabidopsis thaliana 130 Mbp 26,521 JGI 2013?[64] 2013[65]
Cardamine hirsuta (hairy bittercress) strain 'Oxford' Brassicaceae A model system for studies in evolution of plant development 198 Mbp 29,458 8 Max Planck Institute for Plant Breeding Research, Köln, Germany 2016[66] Shotgun sequencing strategy, combining paired end reads (197× assembled sequence coverage) and mate pair reads (66× assembled) from Illumina HiSeq (a total of 52 Gbp raw reads).
Eruca sativa (salad rocket) Brassicaceae Used for food 851 Mbp 45,438 University of Reading 2020[67] Illumina MiSeq and HiSeq2500. PCR free paired end and long mate pair sequencing and assembly. Illumina HiSeq transcriptome sequencing (125/150 bp paired end reads).
Erysimum cheiranthoides (wormseed wallflower) strain 'Elbtalaue' Brassicaceae Model plant for studying defensive chemistry, including cardiac glycosides 175 Mbp 29,947 8 Boyce Thompson Institute, Ithaca, NY 2020[68][69] 39.5 Gb PacBio sequences (average length 10,603 bp), one lane Illumina MiSeq sequencing (2 x 250 bp paired end), Phase Genomics Hi-C scaffolding, PacBio and Illumina transcriptome sequencing
Eutrema salsugineum Brassicaceae A relative of arabidopsis with high salt tolerance 240 Mbp 26,351 JGI 2013[70]
Eutrema parvulum Brassicaceae Comparative analysis of crucifer genomes 2013[57]
Leavenworthia alabamica Brassicaceae Comparative analysis of crucifer genomes 2013[57]
Sisymbrium irio Brassicaceae Comparative analysis of crucifer genomes 2013[57]
Thellungiella parvula Brassicaceae A relative of arabidopsis with high salt tolerance 2011[71]
Cannabis sativa (hemp) Cannabaceae Hemp and marijuana production ca 820 Mbp 30,074 based on transcriptome assembly and clustering 2011[72] Illumina/454

scaffold N50 16.2 Kbp

Capparis spinosa var. herbacea (Caper) Capparaceae Crop 274.53 Mb 21,577 2022[73] contig N50 9.36 Mb
Carica papaya (papaya) Caricaceae Fruit crop 372 Mbp 28,629 2008[74] contig N50 11kbp

scaffold N50

1Mbp

total coverage ~3x (Sanger)

92.1% unigenes mapped

235Mbp anchored (of this 161Mbp also oriented)

Casuarina equisetifolia

(Australian Pine)

Casuarinaceae bonsai subject 300 Mbp 29,827 2018[75]
Tripterygium wilfordii (Lei gong teng) Celastraceae Chinese medicine crop 340.12 Mbp 31,593 2021[76] Contig N50 3.09 Mbp
Cleome gynandra

(African cabbage)

Cleomaceae C4 leafy vegetable and medicinal plant 740 Mb 30,933 2023[77] N50 of 42 Mb
Kalanchoë fedtschenkoi Raym.-Hamet & H. PerrierKalanchoe Crassulaceae Molecular genetic model for obligate CAM species in the eudicots 256 Mbp 30,964 34 2017[78] ~70× paired-end reads and ~37× mate-pair reads generated using an Illumina MiSeq platform.
Rhodiola crenulata (Tibetan medicinal herb) Crassulaceae Uses for medicine and food 344.5 Mb 35,517 2017[79]
Citrullus lanatus (watermelon) Cucurbitaceae Vegetable crop ca 425 Mbp 23,440 BGI 2012[80] 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 450 Mbp 27,427 2012[81] 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[82] contig N50 19.8kbp

scaffold N50 1,140kbp

total coverage ~72.2 (Sanger + Ilumina)

96.8% unigenes mapped

72.8% of the genome anchored

Cucurbita argyrosperma subsp. argyrosperma

(Silver-seed gourd)

Cucurbitaceae Seed and fruit crop 228.8 Mbp 27,998 20 National Autonomous University of Mexico 2019,[83] updated in 2021 contig N50 447 kbp

scaffold N50 11.6 Mbp

total coverage: 120x Illumina (HiSeq2000 and MiSeq) + 31x PacBio RSII

Cucurbita argyrosperma subsp. sororia

(wild gourd)

Cucurbitaceae Wild relative of the silver-seed gourd 255.2 Mbp 30,592 20 National Autonomous University of Mexico 2021[84] contig N50 1.2 Mbp

scaffold N50 12.1 Mbp

total coverage: 213x Illumina HiSeq4000 + 75.4x PacBio Sequel

Siraitia grosvenorii

(Monk fruit)

Cucurbitaceae Chinese medicine/sweetener 456.5 Mbp 30,565 Anhui Agricultural University 2018[85]
Hippophae rhamnoides (sea-buckthorn) Elaeagnaceae used in food and cosmetics 730 Mbp 30,812 2022[86]
Hevea brasiliensis (rubber tree) Euphorbiaceae the most economically important member of the genus Hevea 2013[87]
Jatropha curcas Palawan Euphorbiaceae bio-diesel crop 2011[88]
Manihot esculenta (Cassava) Euphorbiaceae Humanitarian importance ~760 Mb 30,666 JGI 2012[89]
Ricinus communis (Castor bean) Euphorbiaceae Oilseed crop 320 Mbp 31,237 JCVI 2010[90] Sanger coverage~4.6x contig N50 21.1 kbp scaffold N50 496.5kbp
Ricinus communis L. (Wild Castor) Euphorbiaceae one of the most important oil crops worldwide ~318.13 Mb 30,066 National Key R&D Program of China, the National Natural Science Foundation of China, the Guangdong Basic and Applied Basic Research Foundation, China, and the Shenzhen Science and Technology Program, China 2021[91] genome size of 316 Mb, a scaffold N50 of 31.93 Mb, and a contig N50 of 8.96 Mb
Ammopiptanthus nanus Fabaceae Only genus of evergreen broadleaf shrub 889 Mb 37,188 2018[92]
Cajanus cajan (Pigeon pea) var. Asha Fabaceae Model legume 2012[93][94]
Arachis duranensis (A genome diploid wild peanut) accession V14167 Fabaceae Wild ancestor of peanut, an oilseed and grain legume crop 2016[95] Illumina 154x coverage, contig N50 22 kbp, scaffold N50 948 kbp
Amphicarpaea edgeworthii (Chinese hog-peanut) Fabaceae produces both aerial and subterranean fruits 299-Mb 27 899 Taishan Scholar Program, National Natural Science Foundation of China, the Innovation Program of SAAS 2021[96]
Arachis ipaensis (B genome diploid wild peanut) accession K30076 Fabaceae Wild ancestor of peanut, an oilseed and grain legume crop 2016[95] Illumina 163x coverage, contig N50 23 kbp, scaffold N50 5,343 kbp
Cicer arietinum (chickpea) Fabaceae filling 2013[97]
Cicer arietinum L. (chickpea) Fabaceae 2013[98]
Dalbergia odorifera (fragrant rosewood) Fabaceae Wood product (heartwood) and folk medicine 653 Mb 30,310 10 Chinese Academy of Forestry 2020[99] Contig N50: 5.92Mb

Scaffold N50: 56.1 6Mb

Faidherbia albida

(Apple-Ring Acacia)

Fabaceae Importante in the Sahel for raising bees 28,979 2018[100][49]
Glycine max (soybean) var. Williams 82 Fabaceae Protein and oil crop 1115 Mbp 46,430 2010[101] Contig N50:189.4kbp

Scaffold N50:47.8Mbp

Sanger coverage ~8x

WGS

955.1 Mbp assembled

Lablab purpureus

(Hyacinth Bean)

Fabaceae Crop for human consumption 20,946 2018[49][102]
Lotus japonicus (Bird's-foot Trefoil) Fabaceae Model legume 2008[103]
Medicago truncatula (Barrel Medic) Fabaceae Model legume 2011[104]
Melilotus officinalis (sweet yellow clover) Fabaceae Forage and Chinese medicine 976.27 Mbp 50,022 2023[105]
Phaseolus vulgaris (common bean) Fabaceae Model bean 520 Mbp 31,638 JGI 2013?[106]
Prosopis cineraria (Ghaf) Fabaceae Desert mimosoid legume 691 Mbp 55,325 2023[107]
Vicia faba L. (Faba bean) Fabaceae Nature (journal) 2023[108]
Vicia villosa (hairy vetch) Fabaceae Forage and cover crop 2.03 Gbp 2023[109]
Vigna hirtella (Wild vigna) Fabaceae Wild legume 474.1 Mbp 2023[108][110]
Vigna reflexo-pilosa (Créole bean) Fabaceae Tetraploid wild legume 998.7 Mbp 2023[111][112]
Vigna subterranea

(Bambara Groundnut)

Fabaceae similar to peanuts 31,707 2018[113][49]
Vigna trinervia Fabaceae 498,7 Mbp 2023[111]
Trifolium pratense L. (Red clover) Fabaceae often used to relieve symptoms of menopause, high cholesterol, and osteoporosis.[114] 2022[115]
Vicia sativa L. (Common vetch) Fabaceae grain to livestock 2022[116]
Macrotyloma uniflorum (Horse gram) Fabaceae horsefeed 2021[117]
Castanea mollissima (Chinese chestnut) Fagaceae cultivated nut 785.53 Mb 36,479 Beijing University of Agriculture 2019[118] Illumina: ~42.7×

PacBio: ~87× contig N50: 944,000bp

Quercus robur (European oak) Fagaceae Pedunculate oak,

large diversity, somatic mutation studies

736 Mb 25,808 12 Biogeco lab, Inrae, University of Bordeaux 2018[119] https://www.oakgenome.fr/?page_id=587
Carya illinoinensis

Pecan

Junglandaceae snacks in various recipes 651.31 Mb 2019[120]
Juglans mandshurica Maxim. (Manchurian walnut) Junglandaceae cultivated nut 548.7 Mb 2022[121]
Juglans regia (Persian walnut) Junglandaceae cultivated nut 540 Mb Chinese Academy of Forestry 2020[122]
Juglans sigillata (Iron walnut) Junglandaceae cultivated nut 536.50 Mb Nanjing Forestry University 2020[123] Illumina+Nanopore+bionano

scaffold N50: 16.43 Mb, contig N50: 4.34 Mb

Linum usitatissimum (flax) Linaceae Crop ~350 Mbp 43,384 BGI et al. 2012[124]
Bombax ceiba

(red silk cotton tree)

Malvaceae capsules with white fibre like cotton 895 Mb 2018[125]
Durio zibethinus (Durian) Malvaceae Tropical fruit tree ~738 Mbp 2017[126]
Gossypium raimondii Malvaceae One of the putative progenitor species of tetraploid cotton 2013?[127]
Theobroma cacao (cocoa tree) Malvaceae Flavouring crop 2010[128][129]
Theobroma cacao (cocoa tree) cv. Matina 1-6 Malvaceae Most widely cultivated cacao type 2013[130]
Theobroma cacao (200 accessions) Malvaceae domestication history of cacao 2018[131]
Azadirachta indica (neem) Meliaceae Source of number of Terpenoids, including biopesticide azadirachtin, Used in Traditional Medicine 364 Mbp ~20000 GANIT Labs Archived 2014-01-08 at the Wayback Machine 2012[132] and 2011[133] Illumina GAIIx, scaffold N50 of 452028bp, Transcriptome data from Shoot, Root, Leaf, Flower and Seed
Artocarpus nanchuanensis (Bayberry) Moraceae Extremely endangered fruit tree 769.44 Mbp 39,596 28 2022[134]
Moringa oleifera

(Horseradish Tree)

Moringaceae traditional herbal medicine 18,451 2018[135][49]
Eucalyptus caleyi (Caley's ironbark) Myrtaceae 589.32 Mb 2024[136]
Eucalyptus urophylla (Timor white gum) Myrtaceae Fibre and timber crop 544.5 Mb 2023[137]
Eucalyptus grandis (Rose gum) Myrtaceae Fibre and timber crop 691.43 Mb 2011[138][137]
Eucalyptus lansdowneana (crimson mallee) Myrtaceae 633.52 Mb 2024[136]
Eucalyptus marginata (Jarrah) Myrtaceae 512.89 Mb 2024[136]
Eucalyptus pauciflora (Snow gum) Myrtaceae Fibre and timber crop 594.87 Mb ANU 2020[139] Nanopore + Illumina; contig N50: 3.23 Mb
Melaleuca alternifolia (tea tree) Myrtaceae terpene-rich essential oil with therapeutic and cosmetic uses around the world 362 Mb 37,226 Gigabyte, NCBI GenBank, GigaScience 2021[140] 3128 scaffolds with a total length of 362 Mb (N50 = 1.9 Mb)
Averrhoa carambola (Star Fruit) Oxalidales fruit crop 335.49 Mb 2020[141]
Carya cathayensis (Chinese hickory) Rosaceae fruit crop 706.43 Mb 2019[120]
Eriobotrya japonica (Loquat) Rosaceae Fruit tree 760.1 Mb 45,743 Shanghai Academy of Agricultural Sciences 2020[142] Illumina+Nanopore+Hi-C

17 chromosomes, scaffold N50: 39.7 Mb

Fragaria vesca (wild strawberry) Rosaceae Fruit crop 240 Mbp 34,809 2011[143] scaffold N50: 1.3 Mbp

454/Illumina/solid

39x coverage

WGS

Gillenia trifoliata Rosaceae Apple Tribe 320.17±4.22 Mb 26,166 18 2021[144] Number of scaffolds(>2kb): 789, scaffold N50: 30,093,771 bp, Contig N50 (bp): 828,523
Malus domestica (apple) "Golden Delicious" Rosaceae Fruit crop ~742.3 Mbp 57,386 2010[145] contig N50 13.4 (kbp??)

scaffold N50 1,542.7 (kbp??)

total coverage ~16.9x (Sanger + 454)

71.2% anchored

Prunus amygdalus (almond) Rosaceae Fruit crop 2013?[146]
Prunus avium (sweet cherry) cv. Stella Rosaceae Fruit crop 2013?[146]
Prunus mume (Chinese plum or Japanese apricot) Rosaceae Fruit crop 2012[147]
Prunus persica (peach) Rosaceae Fruit crop 265 Mbp 27,852 2013[148] Sanger coverage:8.47x

WGS

ca 99% ESTs mapped

215.9 Mbp in pseudomolecules

Prunus salicina (Japanese plum) Rosaceae Fruit crop 284.2 Mbp 24,448 8 2020[149] PacBio/Hi-C, with contig N50 of 1.78 Mb and scaffold N50 of 32.32 Mb.
Pyrus bretschneideri (ya pear or Chinese white pear) cv. Dangshansuli Rosaceae Fruit crop 2012[150]
Pyrus communis (European pear) cv. Doyenne du Comice Rosaceae Fruit crop 2013?[146]
Rosa roxburghii (Chestnut Rose) Rosaceae Fruit crop 504 Mbp 2023[151]
Rosa sterilis Rosaceae Fruit crop 981.2 Mb 2023[152]
Rubus occidentalis

(Black raspberry)

Rosaceae Fruit crop 290 Mbp 2018[153]
Citrus clementina (Clementine) Rutaceae Fruit crop 2013?[154]
Citrus sinensis (Sweet orange) Rutaceae Fruit crop 2013?,[154] 2013[155]
Clausena lansium (Wampee) Rutaceae Fruit crop 2021[156]
Populus trichocarpa (poplar) Salicaceae Carbon sequestration, model tree, timber 510 Mbp (cytogenetic) 485 Mbp (coverage) 73,013 [Phytozome] 2006[157] Scaffold N50: 19.5 Mbp

Contig N50:552.8 Kbp [phytozome]

WGS

>=95 % cDNA found

Populus pruinosa

(desert tree)

Salicaceae farming and ranching 479.3 Mbp 35,131 2017[158]
Acer truncatum (purpleblow maple) Sapindaceae Tree producing nervonic acid 633.28 Mb 28,438 2020[159] contig N50 = 773.17 Kb; scaffold N50 = 46.36 Mb
Acer yangbiense Sapindaceae Plant species with extremely small populations 110 Gb 28,320 13 2019[160] scaffold N50 = 45 Mb
Dimocarpus longan (Longan) Sapindaceae Fruit crop 471.88 Mb 2017[161]
Xanthoceras sorbifolium Bunge (Yellowhorn) Sapindaceae Fruit Crop 504.2 Mb 24,672 2019[162][163]
Aquilaria sinensis (Agarwood) Thymelaeaceae Fragrant wood 726.5 Mb 29,203 2020[164] Illumina+nanopore+Hi-C, scaffold N50: 88.78 Mb
Vitis vinifera (grape) genotype PN40024 Vitaceae fruit crop 2007[165]
Asterids
[edit]
Organism strain Family Relevance Genome size Number of genes predicted Organization Year of completion Assembly status
Asclepias syriaca, (common milkweed) Apocynaceae Exudes milky latex 420 Mbp 14,474 Oregon State University 2019[166] 80.4× depth

N50 = 3,415 bp

Erigeron breviscapus (Chinese herbal fleabane) Asteraceae Chinese medicine 37,505 2017[167]
Helianthus annuus (sunflower) Asteraceae Oil crop 3.6 Gbb 52,232 INRA and The Sunflower Genome Database[168] 2017[169] N50 contig: 13.7 kb
Lactuca sativa (lettuce) Asteraceae Vegetable crop 2.5 Gbb 38,919 2017[170] N50 contig: 12 kb; N50 scaffold: 476 kb
Handroanthus impetiginosus, Bignoniaceae

(Pink Ipê)

Bignoniaceae Common tree 503.7 Mb 31,668 2017[171]
Diospyros oleifera Cheng (Oil persimmon) Ebenaceae Fruit tree 849.53 Mb 28,580 Zhejiang University & Chinese Academy of Forestry 2019[172] & 2020[173] Two genomes both chromosome scale & assigned to 15 pseudochromosomes
Salvia miltiorrhiza Bunge

(Chinese red sage)

Lamiaceae TCM treatment for COPD 641 Mb 34,598 2015[174]
Callicarpa americana (American beautyberry) Lamiaceae Ornamental shrub and insect-repellent 506 Mb 32,164 Michigan State University 2020[175] 17 pseudomolecules Contig N50: 7.5Mb Scaffold N50: and 29.0 Mb
Mentha x piperita (Peppermint) Lamiaceae Oil crop 353 Mb 35,597 Oregon State University 2017[176]
Tectona grandis

(Teak)

Lamiaceae Durability and water resistance 31,168 2019[177]
Utricularia gibba (humped bladderwort) Lentibulariaceae model system for studying genome size evolution; a carnivorous plant 81.87 Mb 28,494 LANGEBIO, CINVESTAV 2013[178] Scaffold N50: 80.839 Kb
Camptotheca acuminata Decne

(Chinese happy tree)

Nyssaceae chemical drugs for cancer treatment 403 Mb 31,825 2017[179]
Davidia involucrata Baill (Dove tree) Nyssaceae Living fossil 1,169 Mb 42,554 2020[180]
Mimulus guttatus Phrymaceae model system for studying ecological and evolutionary genetics ca 430 Mbp 26,718 JGI 2013?[181] Scaffold N50 = 1.1 Mbp

Contig N50 = 45.5 Kbp

Primula vulgaris (Common primrose) Primulaceae Used for cooking 474 Mb 2018[182]
Cinchona pubescens Vahl. (Fever tree) Rubiaceae Anti-malarial 1.1 Gb 2022[183]
Solanum lycopersicum (tomato) cv. Heinz 1706 Solanaceae Food crop ca 900 Mbp 34,727 SGN 2011[184] 2012[185] Sanger/454/Illumina/Solid

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

over 98% ESTs mappable

Solanum aethiopicum (Ethiopian eggplant) Solanaceae Food crop 1.02 Gbp 34,906 BGI 2019[186] Illumina

scaffold N50: 516,100bp

contig N50: 25,200 bp

~109× coverage

Solanum pimpinellifolium (Currant Tomato) Solanaceae closest wild relative to tomato 2012[185] Illumina

contig N50: 5100bp

~40x coverage

Solanum tuberosum (Potato) Solanaceae Food crop 726 Mbp[187] 39,031 Potato Genome Sequencing Consortium (PGSC) 2011[188][189] 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[190] Illumina

105x coverage

contig N50: 6,506bp

scaffold N50: 44,298bp

Cuscuta campestris

(field dodder)

Solanaceae model system for parasitic plants 556 Mbp kmer (581 Mbp) 44,303 RWTH Aachen University, Research Center Jülich, University of Tromsø, Helmholtz Zentrum München, Technical University Munich, University of Vienna 2018[191] scaffold N50 = 1.38 Mbp
Cuscuta australis (Southern dodder) Solanaceae model system for parasitic plants 265 Mbp

kmer (273 Mbp)

19,671 Kunming Institute of Botany, Chinese Academy of Sciences 2018[192] scaffold N50 = 5.95 Mbp

contig N50 = 3.63 Mbp

Nicotiana benthamiana Solanaceae Close relative of tobacco ca 3 Gbp 2012[193] 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 2.636 Gbp Philip Morris International 2013[194] 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[194] 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[195]

(b) 2014[196]

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[196] N50 contig: 52.2 kb

N50 scaffold: 0.45 Mb

Petunia hybrida Solanaceae Economically important flower 2011[197]

Monocots

[edit]
Grasses
[edit]
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[198]
Aegilops tauschii (Tausch's goatgrass) Poaceae bread wheat D-genome progenitor ca 4.36 Gb 39,622 2017[199] pseudomolecule assembly
Bothriochloa decipiens

(Australian bluestem grass)

Poaceae BCD clade and polyploid 1,218.22 Mb 60,652 2023[200] Scaffold N50: 42.637 Mb
Brachypodium distachyon (purple false brome) Poaceae Model monocot 2010[201]
Coix lacryma-jobi L. (Job's tears) Poaceae Crop & used in medicine & ornamentation 1.619 Gb 39,629 2019[202]
Dichanthelium oligosanthes (Heller's rosette grass) Poaceae C3 grass closely related to C4 species 960 Mb DDPSC 2016[203]
Digitaria exilis (white fonio) Poaceae African orphan crop 761 Mb ICRISAT, UC Davis 2021[204] 3,329 contigs. N50: 1.73 Mb; L50, 126)
Eragrostis curvula Poaceae good for livestock 602 Mb 56,469 2019[205]
Hordeum vulgare (barley) Poaceae Model of ecological adoption IBSC 2012,[206] 2017[207]
Oryza brachyantha (wild rice) Poaceae Disease resistant wild relative of rice 2013[208]
Oryza glaberrima (African rice) var CG14 Poaceae West-African species of rice 2010[209]
Oryza rufipogon (red rice) Poaceae Ancestor to Oryza sativa 406 Mb 37,071 SIBS 2012[210] Illumina HiSeq2000

100x coverage

Oryza sativa (long grain rice) ssp indica Poaceae Crop and model cereal 430 Mb[211] International Rice Genome Sequencing Project (IRGSP) 2002[212]
Oryza sativa (Short grain rice) ssp japonica Poaceae Crop and model cereal 430 Mb International Rice Genome Sequencing Project (IRGSP) 2002[213]
Panicum virgatum (switchgrass) Poaceae biofuel 2013?[214]
Poa annua (annual bluegrass) Poaceae weed 3.56 Gb 76,420 USDA ARS, Forage and Range Research 2023[215] unphased (haploid) pseudomolecules
Poa infirma (weak bluegrass) Poaceae diploid progenitor to Poa annua 2.25 Gb 39,420 Penn State University 2023[216] unphased (haploid) pseudomolecules
Poa pratensis (Kentucky bluegrass) Poaceae Lawn grass 6.09 Gbp 2023[217] Scaffold N50: 65.1 Mbp
Poa supina (supine bluegrass) Poaceae diploid progenitor to Poa annua 1.27 Gb 37,935 Penn State University 2023[216] unphased (haploid) pseudomolecules
Phyllostachys edulis (moso bamboo) Poaceae Bamboo textile industry 603.3 Mb 25,225 2013[218] 2018[219]
Sorghum bicolor genotype BTx623 Poaceae Crop ca 730 Mb 34,496 2009[220] contig N50:195.4kbp

scaffold N50: 62.4Mbp

Sanger, 8.5x coverage

WGS

Triticum aestivum (bread wheat) Poaceae 20% of global nutrition 14.5 Gb 107,891 IWGSC 2018[221] pseudomolecule assembly
Triticum urartu Poaceae Bread wheat A-genome progenitor ca 4.94 Gb BGI 2013[222] Non-repetitive sequence assembled

Illumina WGS

Zea mays (maize) ssp mays B73 Poaceae Cereal crop 2.3 Gb 39,656[223] 2009[224] contig N50 40kbp

scaffold N50: 76kbp

Sanger, 4-6x coverage per BAC

Pennisetum glaucum (pearl millet) Poaceae Sub-Saharan and Sahelian millet species ~1,79 Gb 38,579 2017[225] WGS and bacterial artificial chromosome (BAC) sequencing
Other non-grasses
[edit]
Organism strain Family Relevance Genome size Number of genes predicted No of chromosomes Organization Year of completion Assembly status
Ananas bracteatus accession CB5 Bromeliaceae Wild pineapple relative 382 Mbp 27,024 25 2015[226] 100× coverage using Illumina paired-end reads of libraries with different insert sizes.
Ananas comosus (L.) Merr. (Pineapple), varieties F153 and MD2 Bromeliaceae The most economically valuable crop possessing crassulacean acid metabolism (CAM) 382 Mb 27,024 25 2015[226] 400× Illumina reads, 2× Moleculo synthetic long reads, 1× 454 reads, 5× PacBio single-molecule long reads and 9,400 BACs.
Ottelia alismoides (Duck lettuce) Hydrocharitaceae Aquatic plant 6.45Gb 2024[227] 11,923 scaffolds/contigs and an N50 of 790,733 bp
Pontederia crassipes (Water hyacinth) Pontederiaceae Aquatic plant 1.22 Gb 8 65,299 2024[228] Scaffold N50 = 77.2Mb
Musa acuminata (Banana) Musaceae A-genome of modern banana cultivars 523 Mbp 36,542 2012[229] N50 contig: 43.1 kb

N50 scaffold: 1.3 Mb

Musa balbisiana (Wild banana) (PKW) Musaceae B-genome of modern banana cultivars 438 Mbp 36,638 2013[230] N50 contig: 7.9 kb
Musa balbisiana (DH-PKW) Musaceae B-genome (B-subgenome to cultivated allotriploid bananas) 430 Mb 35,148 11 CATAS, BGI, CIRAD 2019[231] N50 contig: 1.83 Mb
Musa beccarii (Red ornamental banana) Musaceae Ornamental, aids understanding Musaceae genomes evolution 567 Mb 39,112 9 2023[232]
Calamus simplicifolius
 Arecaceae native to tropical and subtropical regions 1.98 Gb 51,235 2018[233]
Cocos nucifera (Coconut palm) Arecaceae used in food and cosmetics ~2.42 Gb 2017[234]
Daemonorops jenkinsiana Arecaceae native to tropical and subtropical regions. 1.61 Gb 52,342 2018[233]
Phoenix dactylifera (Date palm) Arecaceae Woody crop in arid regions 658 Mbp 28,800 2011[235] N50 contig: 6.4 kb
Elaeis guineensis (African oil palm) Arecaceae Oil-bearing crop ~1800 Mbp 34,800 2013[236] N50 scaffold: 1.27 Mb
Spirodela polyrhiza (Greater duckweed) Araceae Aquatic plant 158 Mbp 19,623 2014[237] N50 scaffold: 3.76 Mb
Dendrobium hybrid cultivar ‘Emma White’ Orchidaceae Commercialised hybrid orchid 678 Mbp 2022[238]
Phalaenopsis equestris (Schauer) Rchb.f. (Moth orchid) Orchidaceae Breeding parent of many modern moth orchid cultivars and hybrids.

Plant with crassulacean acid metabolism (CAM).

1600 Mbp 29,431 2014[239] N50 scaffold: 359,115 kb
Iris pallida Lam. (Dalmatian Iris) Iridaceae Ornamental and, commercial interest in secondary metabolites 10.04 Gbp 63,944 Novartis 2023[240] Scaffold N50: 14.34 Mbp
Iris sibirica (Siberian Ibis) Iridaceae Ornamental flower 2023[241]
Iris virginica (Southern Blue Flag Iris) Iridaceae Ornamental flower 2023[241]

Press releases announcing sequencing

[edit]

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 peer-review journal with DOI.

See also

[edit]
[edit]

References

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