List of sequenced plant genomes

Last updated

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.

Contents

See also List of sequenced algae genomes.

Bryophytes

Organism strainDivisionRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Anthoceros angustus Bryophytes Early diverging land plant
Ceratodon purpureus Bryophytes Early diverging land plant
Fontinalis antipyretica (greater water-moss) Bryophytes Aquatic moss385.2 Mbp16,538 BGI 2020 [1] BGISEQ-500 & 10X, scaffold N50 45.8 Kbp
Marchantia polymorpha Bryophytes Early diverging land plant225.8 Mb19,1382017 [2]
Physcomitrella patens ssp. patens str. Gransden 2004 Bryophytes Early diverging land plant462.3 Mbp35,9382008 [3]
Pleurozium schreberi (feather moss) Bryophytes Ubiquitous moss species318 Mbp15,9922019 [4]

Vascular plants

Lycophytes

Organism strainDivisionRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Selaginella moellendorffii Lycopodiophyta Model organism106 Mb22,2852011 [5] [6] scaffold N50 = 1.7 Mb
Selaginella lepidophylla Lycopodiophyta Desiccation tolerance122 Mb27,2042018 [7] contig N50 = 163 kb

Ferns

Organism strainDivisionRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Azolla filiculoides Polypodiophyta Fern0.75 Gb20,2012018 [8]
Salvinia cucullata Polypodiophyta Fern0.26 Gb19,9142018 [8]
Ceratopteris richardii Polypodiophyta Model organism7.5 Gb36,8572019 (v1.1), [9] 2021 (v2.1) [10] Partial assembly consisting of 7.5 Gb/11.2 Gb, arranged in 39 chromosomes
Alsophila spinulosa Polypodiophyta Tree Fern6.23 Gb67,8312022 [11]

Gymnosperms

Organism strainDivisionRelevanceGenome sizeNumber of genes predictedNo of chromosomesOrganizationYear of completionAssembly status
Cycas panzhihuaensis (Dukou sago palm) Cycadophyta Rare and vulnerable species of cycad10.5 Gb2022 [12]
Picea abies (Norway spruce) Pinales Timber, tonewood, ornamental such as Christmas tree 19.6 Gb26,359 [13] 12Umeå Plant Science Centre / SciLifeLab, Sweden2013 [14]
Picea glauca (White spruce) Pinales Timber, Pulp20.8 Gb14,462 [13] 12Institutional Collaboration2013 [15] [16]
Pinus taeda (Loblolly pine) Pinales Timber20.15 Gb9,024 [13] 122014 [17] [18] [19] N50 scaffold size: 66.9 kbp
Pinus lambertiana (Sugar pine) Pinales Timber; with the largest genomes among the pines;

the largest pine species

31 Gb13,936122016 [13] 61.5X sequence coverage, platforms used:

Hiseq 2000, Hiseq 2500, GAIIx, MiSeq

Ginkgo biloba Ginkgoales 11.75 Gb41,8402016 [20] N50 scaffold size: 48.2 kbp
Pseudotsuga menziesii Pinales 16 Gb54,830132017 [21] N50 scaffold size : 340.7 kbp
Gnetum monatum Gnetales 4.07 Gb27,4912018 [22]
Larix sibirica Pinales 12.34 Gbp2019 [23] scaffold N50 of 6440 bp
Abies alba Pinales 18.16 Gb94,2052019 [24] scaffold N50 of 14,051 bp

Angiosperms

Amborellales

Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Amborella trichopoda Amborellaceae Basal angiosperm2013 [25] [26]

Chlorantales

Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Chloranthus spicatus (Thunb.) Makino, [27] (Pearl Orchid)Chlorantaceae2021 [28] saffold N50 of 191.37 Mb

Magnoliales

Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Annona muricata Annonaceae Commercially grown fruit, medicinal applications799.11 Mb23,375 Institute for Biodiversity and Environmental Research (UBD)

Alliance for Conservation Tree Genomics

Biodiversity Genomics Team

2021 [29] 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 species338.93 Mb33,2292022 [30] Contig N50 of 1.68 Mb
Cinnamomum kanehirae (Stout camphor tree) Lauraceae 730.7 Mb2019 [31]

Eudicots

Proteales
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Macadamia integrifolia HAES 741 (Macadamia nut) Proteaceae Commercially grown nut745 Mb34,2742020 [32] N50 413 kb
Macadamia jansenii Proteaceae Rare relative of macademia nut750 Mbp2020 [33] Compared Nanopore, Illumina and BGI stLRF data
Nelumbo nucifera (sacred lotus) Nelumbonaceae Basal eudicot929 Mbp2013 [34] contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp
Ranunculales
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Aquilegia coerulea Ranunculaceae Basal eudicotUnpublished [35]
Trochodendrales
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Trochodendron aralioides (Wheel tree) Trochodendrales Basal eudicot having secondary xylem without vessel elements1.614 Gb35,328 Guangxi University 2019 [36] 19 scaffolds corresponding to 19 chromosomes
Caryophyllales
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Beta vulgaris (sugar beet) Chenopodiaceae Crop plant714–758 Mbp27,4212013 [37]
Chenopodium quinoa Chenopodiaceae Crop plant1.39–1.50 Gb44,7762017 [38] 3,486 scaffolds, scaffold N50 of 3.84 Mb, 90% of the assembled genome is contained in 439 scaffolds [38]
Amaranthus hypocondriacus Amaranthaceae Crop plant403.9 Mb23,8472016 [39] 16 large scaffolds from 16.9 to 38.1 Mb. N50 and L50 of the assembly was 24.4 Mb and 7, respectively. [40]
Carnegiea gigantea Cactaceae Wild plant1.40 Gb28,2922017 [41] 57,409 scaffolds, scaffold N50 of 61.5 kb [41]
Suaeda aralocaspica Amaranthaceae Performs complete C4 photosynthesis within individual cells (SCC4)467 Mb29,604ABLife Inc.2019 [42] 4,033 scaffolds, scaffold N50 length of 1.83 Mb
Simmondsia chinensis (jojoba) Simmondsiaceae Oilseed Crop887 Mb23,4902020 [43] 994 scaffolds, scaffold N50 length of 5.2 Mb

Drosera capensis

Droseraceae Carnivorous Plant263.79 Mb2016 [44] 12,713 scaffolds [44]
Tamarix chinensis (Chinese tamarisk) Tamaricaceae Margin tree1.32 Gb2023 [45]
Rosids
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedNo of chromosomesOrganizationYear of completionAssembly status
Bretschneidera sinensis Akaniaceae endangered relic tree species1.21 Gb45,8392022 [46]
Sclerocarya birrea

(Marula)

Anacardiaceae Used for food18,3972018 [47] [48]
Betula pendula (silver birch) Betulaceae Boreal forest tree, model for forest biotechnology435 Mbp [49] 28,39914University of Helsinki2017 [49] 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 species430 Mbp2021 [50] contig N50 = 751 kbp
Betula nana (dwarf birch) Betulaceae Arctic shrub450 Mbp QMUL/SBCS 2013 [51]
Corylus heterophylla Fisch (Asian hazel) Betulaceae Nut tree used for food370.75 Mbp27,591112021 [52] 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 breeding367.67 Mb28,409112021 [53]
Aethionema arabicum Brassicaceae Comparative analysis of crucifer genomes2013 [54]
Arabidopsis lyrata ssp. lyrata strain MN47 Brassicaceae Model plant206.7 Mbp32,670 [55] 82011 [55] 8.3X sequence coverage, analyzed on ABI 3730XL capillary sequencers
Arabidopsis thaliana Ecotype:Columbia Brassicaceae Model plant135 Mbp27,655 [56] 5AGI2000 [57]
Barbarea vulgaris

G-type

Brassicaceae Model plant for specialised metabolites and plant defenses167.7 Mbp25,35082017 [58] 66.5 X coverage with Illumina GA II technology
Brassica rapa ssp. pekinensis (Chinese cabbage) accession Chiifu-401-42 Brassicaceae Assorted crops and model organism485 Mbp41,174 (has undergone genome triplication)10The Brassica rapa Genome Sequencing Project Consortium2011 [59] 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 Crops1130 Mbp101,04019Institutional Collaboration2014 [60] 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 thaliana130 Mbp26,521JGI2013? [61] 2013 [62]
Cardamine hirsuta (hairy bittercress) strain 'Oxford' Brassicaceae A model system for studies in evolution of plant development198 Mbp29,4588Max Planck Institute for Plant Breeding Research, Köln, Germany2016 [63] 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 food851 Mbp45,438 University of Reading 2020 [64] 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 Mbp29,9478Boyce Thompson Institute, Ithaca, NY2020 [65] [66] 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 tolerance240 Mbp26,351JGI2013 [67]
Eutrema parvulum Brassicaceae Comparative analysis of crucifer genomes2013 [54]
Leavenworthia alabamica Brassicaceae Comparative analysis of crucifer genomes2013 [54]
Sisymbrium irio Brassicaceae Comparative analysis of crucifer genomes2013 [54]
Thellungiella parvula Brassicaceae A relative of arabidopsis with high salt tolerance2011 [68]
Cannabis sativa (hemp) Cannabaceae Hemp and marijuana productionca 820 Mbp30,074 based on transcriptome assembly and clustering2011 [69] Illumina/454

scaffold N50 16.2 Kbp

Capparis spinosa var. herbacea (Caper) Capparaceae Crop274.53 Mb21,5772022 [70] contig N50 9.36 Mb
Carica papaya (papaya) Caricaceae Fruit crop372 Mbp28,6292008 [71] 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 subject300 Mbp29,8272018 [72]
Tripterygium wilfordii (Lei gong teng) Celastraceae Chinese medicine crop340.12 Mbp31,5932021 [73] Contig N50 3.09 Mbp
Cleome gynandra

(African cabbage)

Cleomaceae C4 leafy vegetable and medicinal plant740 Mb30,9332023 [74] N50 of 42 Mb
Kalanchoë fedtschenkoi Raym.-Hamet & H. PerrierKalanchoe Crassulaceae Molecular genetic model for obligate CAM species in the eudicots256 Mbp30,964342017 [75] ~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 food344.5 Mb35,5172017 [76]
Citrullus lanatus (watermelon) Cucurbitaceae Vegetable cropca 425 Mbp23,440 BGI 2012 [77] 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 crop450 Mbp27,4272012 [78] 454

13.5x coverage

contig N50: 18.1kbp

scaffold N50: 4.677 Mbp

WGS

Cucumis sativus (cucumber) 'Chinese long' inbred line 9930 Cucurbitaceae Vegetable crop350 Mbp (Kmer depth) 367 Mbp (flow cytometry)26,6822009 [79] 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 crop228.8 Mbp27,99820 National Autonomous University of Mexico 2019, [80] updated in 2021contig 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 gourd255.2 Mbp30,59220 National Autonomous University of Mexico 2021 [81] 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/sweetener456.5 Mbp30,565Anhui Agricultural University2018 [82]
Hippophae rhamnoides (sea-buckthorn) Elaeagnaceae used in food and cosmetics730 Mbp30,8122022 [83]
Hevea brasiliensis (rubber tree) Euphorbiaceae the most economically important member of the genus Hevea 2013 [84]
Jatropha curcas Palawan Euphorbiaceae bio-diesel crop2011 [85]
Manihot esculenta (Cassava) Euphorbiaceae Humanitarian importance~760 Mb30,666JGI2012 [86]
Ricinus communis (Castor bean) Euphorbiaceae Oilseed crop320 Mbp31,237JCVI2010 [87] 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 Mb30,066National 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, China2021 [88] 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 shrub889 Mb37,1882018 [89]
Cajanus cajan (Pigeon pea) var. Asha Fabaceae Model legume2012 [90] [91]
Arachis duranensis (A genome diploid wild peanut) accession V14167 Fabaceae Wild ancestor of peanut, an oilseed and grain legume crop2016 [92] Illumina 154x coverage, contig N50 22 kbp, scaffold N50 948 kbp
Amphicarpaea edgeworthii (Chinese hog-peanut) Fabaceae produces both aerial and subterranean fruits299-Mb27 899Taishan Scholar Program, National Natural Science Foundation of China, the Innovation Program of SAAS2021 [93]
Arachis ipaensis (B genome diploid wild peanut) accession K30076 Fabaceae Wild ancestor of peanut, an oilseed and grain legume crop2016 [92] Illumina 163x coverage, contig N50 23 kbp, scaffold N50 5,343 kbp
Cicer arietinum (chickpea) Fabaceae filling2013 [94]
Cicer arietinum L. (chickpea) Fabaceae 2013 [95]
Dalbergia odorifera (fragrant rosewood) Fabaceae Wood product (heartwood) and folk medicine653 Mb30,31010Chinese Academy of Forestry2020 [96] Contig N50: 5.92Mb

Scaffold N50: 56.1 6Mb

Faidherbia albida

(Apple-Ring Acacia)

Fabaceae Importante in the Sahel for raising bees28,9792018 [97] [47]
Glycine max (soybean) var. Williams 82 Fabaceae Protein and oil crop1115 Mbp46,4302010 [98] Contig N50:189.4kbp

Scaffold N50:47.8Mbp

Sanger coverage ~8x

WGS

955.1 Mbp assembled

Lablab purpureus

(Hyacinth Bean)

Fabaceae Crop for human consumption20,9462018 [47] [99]
Lotus japonicus (Bird's-foot Trefoil) Fabaceae Model legume2008 [100]
Medicago truncatula (Barrel Medic) Fabaceae Model legume2011 [101]
Melilotus officinalis (sweet yellow clover) Fabaceae Forage and Chinese medicine976.27 Mbp50,0222023 [102]
Phaseolus vulgaris (common bean) Fabaceae Model bean520 Mbp31,638JGI2013? [103]
Prosopis cineraria (Ghaf) Fabaceae Desert mimosoid legume691 Mbp55,3252023 [104]
Vicia faba L. (Faba bean) Fabaceae Nature (journal) 2023 [105]
Vicia villosa (hairy vetch) Fabaceae Forage and cover crop2.03 Gbp2023 [106]
Vigna hirtella (Wild vigna) Fabaceae Wild legume474.1 Mbp2023 [105] [107]
Vigna reflexo-pilosa (Créole bean) Fabaceae Tetraploid wild legume998.7 Mbp2023 [108] [109]
Vigna subterranea

(Bambara Groundnut)

Fabaceae similar to peanuts31,7072018 [110] [47]
Vigna trinervia Fabaceae 498,7 Mbp2023 [108]
Trifolium pratense L. (Red clover) Fabaceae often used to relieve symptoms of menopause, high cholesterol, and osteoporosis. [111] 2022 [112]
Vicia sativa L. (Common vetch) Fabaceae grain to livestock2022 [113]
Macrotyloma uniflorum (Horse gram) Fabaceae horsefeed2021 [114]
Castanea mollissima (Chinese chestnut) Fagaceae cultivated nut785.53 Mb36,479Beijing University of Agriculture2019 [115] Illumina: ~42.7×

PacBio: ~87× contig N50: 944,000bp

Quercus robur (European oak) Fagaceae Pedunculate oak,

large diversity, somatic mutation studies

736 Mb25,80812 Biogeco lab, Inrae, University of Bordeaux 2018 [116] https://www.oakgenome.fr/?page_id=587
Carya illinoinensis

Pecan

Junglandaceae snacks in various recipes651.31 Mb2019 [117]
Juglans mandshurica Maxim. (Manchurian walnut) Junglandaceae cultivated nut548.7 Mb2022 [118]
Juglans regia (Persian walnut) Junglandaceae cultivated nut540 MbChinese Academy of Forestry2020 [119]
Juglans sigillata (Iron walnut) Junglandaceae cultivated nut536.50 Mb Nanjing Forestry University 2020 [120] Illumina+Nanopore+bionano

scaffold N50: 16.43 Mb, contig N50: 4.34 Mb

Linum usitatissimum (flax) Linaceae Crop~350 Mbp43,384 BGI et al.2012 [121]
Bombax ceiba

(red silk cotton tree)

Malvaceae capsules with white fibre like cotton895 Mb2018 [122]
Durio zibethinus (Durian) Malvaceae Tropical fruit tree~738 Mbp2017 [123]
Gossypium raimondii Malvaceae One of the putative progenitor species of tetraploid cotton2013? [124]
Theobroma cacao (cocoa tree) Malvaceae Flavouring crop2010 [125] [126]
Theobroma cacao (cocoa tree) cv. Matina 1-6 Malvaceae Most widely cultivated cacao type2013 [127]
Theobroma cacao (200 accessions) Malvaceae domestication history of cacao2018 [128]
Azadirachta indica (neem) Meliaceae Source of number of Terpenoids, including biopesticide azadirachtin, Used in Traditional Medicine364 Mbp~20000 GANIT Labs Archived 2014-01-08 at the Wayback Machine 2012 [129] and 2011 [130] Illumina GAIIx, scaffold N50 of 452028bp, Transcriptome data from Shoot, Root, Leaf, Flower and Seed
Artocarpus nanchuanensis (Bayberry) Moraceae Extremely endangered fruit tree769.44 Mbp39,596282022 [131]
Moringa oleifera

(Horseradish Tree)

Moringaceae traditional herbal medicine18,4512018 [132] [47]
Eucalyptus grandis (Rose gum) Myrtaceae Fibre and timber crop691.43 Mb2011 [133]
Eucalyptus pauciflora (Snow gum) Myrtaceae Fibre and timber crop594.87 Mb ANU 2020 [134] Nanopore + Illumina; contig N50: 3.23 Mb
Melaleuca alternifolia (tea tree) Myrtaceae terpene-rich essential oil with therapeutic and cosmetic uses around the world362 Mb37,226 Gigabyte, NCBI GenBank, GigaScience 2021 [135] 3128 scaffolds with a total length of 362 Mb (N50 = 1.9 Mb)
Averrhoa carambola (Star Fruit) Oxalidales fruit crop335.49 Mb2020 [136]
C. cathayensis

(Chinese hickory)

Rosaceae fruit crop706.43 Mb2019 [117]
Eriobotrya japonica (Loquat) Rosaceae Fruit tree760.1 Mb45,743Shanghai Academy of Agricultural Sciences2020 [137] Illumina+Nanopore+Hi-C

17 chromosomes, scaffold N50: 39.7 Mb

Fragaria vesca (wild strawberry) Rosaceae Fruit crop240 Mbp34,8092011 [138] scaffold N50: 1.3 Mbp

454/Illumina/solid

39x coverage

WGS

Gillenia trifoliata Rosaceae Apple Tribe320.17±4.22 Mb26,166182021 [139] 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 Mbp57,3862010 [140] 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 crop2013? [141]
Prunus avium (sweet cherry) cv. Stella Rosaceae Fruit crop2013? [141]
Prunus mume (Chinese plum or Japanese apricot) Rosaceae Fruit crop2012 [142]
Prunus persica (peach) Rosaceae Fruit crop265 Mbp27,8522013 [143] Sanger coverage:8.47x

WGS

ca 99% ESTs mapped

215.9 Mbp in pseudomolecules

Prunus salicina (Japanese plum) Rosaceae Fruit crop284.2 Mbp24,44882020 [144] 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 crop2012 [145]
Pyrus communis (European pear) cv. Doyenne du Comice Rosaceae Fruit crop2013? [141]
Rosa roxburghii (Chestnut Rose) Rosaceae Fruit crop504 Mbp2023 [146]
Rosa sterilis Rosaceae Fruit crop981.2 Mb2023 [147]
Rubus occidentalis

(Black raspberry)

Rosaceae Fruit crop290 Mbp2018 [148]
Citrus clementina (Clementine) Rutaceae Fruit crop2013? [149]
Citrus sinensis (Sweet orange) Rutaceae Fruit crop2013?, [149] 2013 [150]
Clausena lansium (Wampee)RutaceaeFruit crop2021 [151]
Populus trichocarpa (poplar) Salicaceae Carbon sequestration, model tree, timber510 Mbp (cytogenetic) 485 Mbp (coverage)73,013 [Phytozome]2006 [152] Scaffold N50: 19.5 Mbp

Contig N50:552.8 Kbp [phytozome]

WGS

>=95 % cDNA found

Populus pruinosa

(desert tree)

Salicaceae farming and ranching479.3 Mbp35,1312017 [153]
Acer truncatum (purpleblow maple) Sapindaceae Tree producing nervonic acid633.28 Mb28,4382020 [154] contig N50 = 773.17 Kb; scaffold N50 = 46.36 Mb
Acer yangbiense Sapindaceae Plant species with extremely small populations110 Gb28,320132019 [155] scaffold N50 = 45 Mb
Dimocarpus longan (Longan) Sapindaceae Fruit crop471.88 Mb2017 [156]
Xanthoceras sorbifolium Bunge (Yellowhorn) Sapindaceae Fruit Crop504.2 Mb24,6722019 [157] [158]
Aquilaria sinensis (Agarwood) Thymelaeaceae Fragrant wood726.5 Mb29,2032020 [159] Illumina+nanopore+Hi-C, scaffold N50: 88.78 Mb
Vitis vinifera (grape) genotype PN40024 Vitaceae fruit crop2007 [160]
Asterids
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Asclepias syriaca , (common milkweed) Apocynaceae Exudes milky latex420 Mbp14,474 Oregon State University 2019 [161] 80.4× depth

N50 = 3,415 bp

Erigeron breviscapus (Chinese herbal fleabane) Asteraceae Chinese medicine37,5052017 [162]
Helianthus annuus (sunflower) Asteraceae Oil crop3.6 Gbb52,232 INRA and The Sunflower Genome Database [163] 2017 [164] N50 contig: 13.7 kb
Lactuca sativa (lettuce) Asteraceae Vegetable crop2.5 Gbb38,9192017 [165] N50 contig: 12 kb; N50 scaffold: 476 kb
Handroanthus impetiginosus, Bignoniaceae

(Pink Ipê)

Bignoniaceae Common tree503.7 Mb31,6682017 [166]
Diospyros oleifera Cheng (Oil persimmon) Ebenaceae Fruit tree849.53 Mb28,580 Zhejiang University & Chinese Academy of Forestry2019 [167] & 2020 [168] Two genomes both chromosome scale & assigned to 15 pseudochromosomes
Salvia miltiorrhiza Bunge

(Chinese red sage)

Lamiaceae TCM treatment for COPD641 Mb34,5982015 [169]
Callicarpa americana (American beautyberry) Lamiaceae Ornamental shrub and insect-repellent506 Mb32,164 Michigan State University 2020 [170] 17 pseudomolecules Contig N50: 7.5Mb Scaffold N50: and 29.0 Mb
Mentha x piperita (Peppermint) Lamiaceae Oil crop353 Mb35,597 Oregon State University 2017 [171]
Tectona grandis

(Teak)

Lamiaceae Durability and water resistance31,1682019 [172]
Utricularia gibba (humped bladderwort) Lentibulariaceae model system for studying genome size evolution; a carnivorous plant81.87 Mb28,494LANGEBIO, CINVESTAV2013 [173] Scaffold N50: 80.839 Kb
Camptotheca acuminata Decne

(Chinese happy tree)

Nyssaceae chemical drugs for cancer treatment403 Mb31,8252017 [174]
Davidia involucrata Baill (Dove tree) Nyssaceae Living fossil1,169 Mb42,5542020 [175]
Mimulus guttatus Phrymaceae model system for studying ecological and evolutionary geneticsca 430 Mbp26,718JGI2013? [176] Scaffold N50 = 1.1 Mbp

Contig N50 = 45.5 Kbp

Primula vulgaris (Common primrose) Primulaceae Used for cooking474 Mb2018 [177]
Cinchona pubescens Vahl. (Fever tree) Rubiaceae Anti-malarial1.1 Gb2022 [178]
Solanum lycopersicum (tomato) cv. Heinz 1706 Solanaceae Food cropca 900 Mbp34,727SGN2011 [179] 2012 [180] 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 crop1.02 Gbp34,906 BGI 2019 [181] Illumina

scaffold N50: 516,100bp

contig N50: 25,200 bp

~109× coverage

Solanum pimpinellifolium (Currant Tomato) Solanaceae closest wild relative to tomato2012 [180] Illumina

contig N50: 5100bp

~40x coverage

Solanum tuberosum (Potato) Solanaceae Food crop726 Mbp [182] 39,031Potato Genome Sequencing Consortium (PGSC)2011 [183] [184] Sanger/454/Illumina

79.2x coverage

contig N50: 31,429bp

scaffold N50: 1,318,511bp

Solanum commersonii (commerson's nightshade) Solanaceae Wild potato relative838 Mbp kmer (840 Mbp)37,662UNINA, UMN, UNIVR, Sequentia Biotech, CGR2015 [185] 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 [186] 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 [187] scaffold N50 = 5.95 Mbp

contig N50 = 3.63 Mbp

Nicotiana benthamiana Solanaceae Close relative of tobaccoca 3 Gbp2012 [188] 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 production2.636 GbpPhilip Morris International2013 [189] 94x coverage

scaffold N50: 79.7 kbp

194kbp superscaffolds using physical Nicotiana map

Nicotiana tomentosiformis Solanaceae Tobacco progenitor2.682 GbPhilip Morris International2013 [189] 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 [190]

(b) 2014 [191]

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 Gbp34,4762014 [191] N50 contig: 52.2 kb

N50 scaffold: 0.45 Mb

Petunia hybrida Solanaceae Economically important flower2011 [192]

Monocots

Grasses
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedOrganizationYear of completionAssembly status
Setaria italica (Foxtail millet) Poaceae Model of C4 metabolism2012 [193]
Aegilops tauschii (Tausch's goatgrass) Poaceae bread wheat D-genome progenitorca 4.36 Gb39,6222017 [194] pseudomolecule assembly
Bothriochloa decipiens

(Australian bluestem grass)

Poaceae BCD clade and polyploid1,218.22 Mb60,6522023 [195] Scaffold N50: 42.637 Mb
Brachypodium distachyon (purple false brome) Poaceae Model monocot2010 [196]
Coix lacryma-jobi L. (Job's tears) Poaceae Crop & used in medicine & ornamentation1.619 Gb39,6292019 [197]
Dichanthelium oligosanthes (Heller's rosette grass) Poaceae C3 grass closely related to C4 species960 Mb DDPSC 2016 [198]
Digitaria exilis (white fonio) Poaceae African orphan crop761 Mb ICRISAT, UC Davis 2021 [199] 3,329 contigs. N50: 1.73 Mb; L50, 126)
Eragrostis curvula Poaceae good for livestock602 Mb56,4692019 [200]
Hordeum vulgare (barley) Poaceae Model of ecological adoptionIBSC2012, [201] 2017 [202]
Oryza brachyantha (wild rice) Poaceae Disease resistant wild relative of rice2013 [203]
Oryza glaberrima (African rice) var CG14 Poaceae West-African species of rice2010 [204]
Oryza rufipogon (red rice) Poaceae Ancestor to Oryza sativa 406 Mb37,071SIBS2012 [205] Illumina HiSeq2000

100x coverage

Oryza sativa (long grain rice) ssp indica Poaceae Crop and model cereal430 Mb [206] International Rice Genome Sequencing Project (IRGSP)2002 [207]
Oryza sativa (Short grain rice) ssp japonica Poaceae Crop and model cereal430 MbInternational Rice Genome Sequencing Project (IRGSP)2002 [208]
Panicum virgatum (switchgrass) Poaceae biofuel2013? [209]
Poa annua (annual bluegrass) Poaceae weed3.56 Gb76,420 USDA ARS, Forage and Range Research2023 [210] unphased (haploid) pseudomolecules
Poa infirma (weak bluegrass) Poaceae diploid progenitor to Poa annua 2.25 Gb39,420 Penn State University 2023 [211] unphased (haploid) pseudomolecules
Poa pratensis (Kentucky bluegrass) Poaceae Lawn grass6.09 Gbp2023 [212] Scaffold N50: 65.1 Mbp
Poa supina (supine bluegrass) Poaceae diploid progenitor to Poa annua 1.27 Gb37,935 Penn State University 2023 [211] unphased (haploid) pseudomolecules
Phyllostachys edulis (moso bamboo) Poaceae Bamboo textile industry603.3 Mb25,2252013 [213] 2018 [214]
Sorghum bicolor genotype BTx623 Poaceae Cropca 730 Mb34,4962009 [215] contig N50:195.4kbp

scaffold N50: 62.4Mbp

Sanger, 8.5x coverage

WGS

Triticum aestivum (bread wheat) Poaceae 20% of global nutrition14.5 Gb107,891IWGSC2018 [216] pseudomolecule assembly
Triticum urartu Poaceae Bread wheat A-genome progenitorca 4.94 Gb BGI 2013 [217] Non-repetitive sequence assembled

Illumina WGS

Zea mays (maize) ssp mays B73 Poaceae Cereal crop2.3 Gb39,656 [218] 2009 [219] 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 Gb38,5792017 [220] WGS and bacterial artificial chromosome (BAC) sequencing
Other non-grasses
Organism strainFamilyRelevanceGenome sizeNumber of genes predictedNo of chromosomesOrganizationYear of completionAssembly status
Ananas bracteatus accession CB5 Bromeliaceae Wild pineapple relative382 Mbp27,024252015 [221] 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 Mb27,024252015 [221] 400× Illumina reads, 2× Moleculo synthetic long reads, 1× 454 reads, 5× PacBio single-molecule long reads and 9,400 BACs.
Musa acuminata (Banana) Musaceae A-genome of modern banana cultivars523 Mbp36,5422012 [222] N50 contig: 43.1 kb

N50 scaffold: 1.3 Mb

Musa balbisiana (Wild banana) (PKW) Musaceae B-genome of modern banana cultivars438 Mbp36,6382013 [223] N50 contig: 7.9 kb
Musa balbisiana (DH-PKW) Musaceae B-genome (B-subgenome to cultivated allotriploid bananas)430 Mb35,14811 CATAS, BGI, CIRAD 2019 [224] N50 contig: 1.83 Mb
Musa beccarii (Red ornamental banana) Musaceae Ornamental, aids understanding Musaceae genomes evolution567 Mb39,11292023 [225]
Calamus simplicifolius
Arecaceae native to tropical and subtropical regions1.98 Gb51,2352018 [226]
Cocos nucifera (Coconut palm) Arecaceae used in food and cosmetics~2.42 Gb2017 [227]
Daemonorops jenkinsiana Arecaceae native to tropical and subtropical regions.1.61 Gb52,3422018 [226]
Phoenix dactylifera (Date palm) Arecaceae Woody crop in arid regions658 Mbp28,8002011 [228] N50 contig: 6.4 kb
Elaeis guineensis (African oil palm) Arecaceae Oil-bearing crop~1800 Mbp34,8002013 [229] N50 scaffold: 1.27 Mb
Spirodela polyrhiza (Greater duckweed) Araceae Aquatic plant158 Mbp19,6232014 [230] N50 scaffold: 3.76 Mb
Dendrobium hybrid cultivar ‘Emma White’ Orchidaceae Commercialised hybrid orchid678 Mbp2022 [231]
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 Mbp29,4312014 [232] N50 scaffold: 359,115 kb
Iris pallida Lam. (Dalmatian Iris) Iridaceae Ornamental and, commercial interest in secondary metabolites10.04 Gbp63,944 Novartis 2023 [233] Scaffold N50: 14.34 Mbp
Iris sibirica (Siberian Ibis) Iridaceae Ornamental flower2023 [234]
Iris virginica (Southern Blue Flag Iris) Iridaceae Ornamental flower2023 [234]

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 peer-review journal with DOI.

See also

Related Research Articles

<span class="mw-page-title-main">Genome project</span>

Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.

<span class="mw-page-title-main">CRISPR</span> Family of DNA sequence found in prokaryotic organisms

CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacteriophages that had previously infected the prokaryote. They are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.

Zinc-finger nucleases (ZFNs) are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target specific desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes. By taking advantage of endogenous DNA repair machinery, these reagents can be used to precisely alter the genomes of higher organisms. Alongside CRISPR/Cas9 and TALEN, ZFN is a prominent tool in the field of genome editing.

<span class="mw-page-title-main">Prasinophyte</span> Class of algae

The prasinophytes are a group of unicellular green algae. Prasinophytes mainly include marine planktonic species, as well as some freshwater representatives. The prasinophytes are morphologically diverse, including flagellates with one to eight flagella and non-motile (coccoid) unicells. The cells of many species are covered with organic body scales; others are naked. Well studied genera include Ostreococcus, considered to be the smallest free-living eukaryote, and Micromonas, both of which are found in marine waters worldwide. Prasinophytes have simple cellular structures, containing a single chloroplast and a single mitochondrion. The genomes are relatively small compared to other eukaryotes . At least one species, the Antarctic form Pyramimonas gelidicola, is capable of phagocytosis and is therefore a mixotrophic algae.

<span class="mw-page-title-main">Neoaves</span> Clade of birds

Neoaves is a clade that consists of all modern birds with the exception of Palaeognathae and Galloanserae. Almost 95% of the roughly 10,000 known species of extant birds belong to the Neoaves.

<span class="mw-page-title-main">Pan-genome</span> All genes of all strains in a clade

In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. More generally, it is the union of all the genomes of a clade. The pan-genome can be broken down into a "core pangenome" that contains genes present in all individuals, a "shell pangenome" that contains genes present in two or more strains, and a "cloud pangenome" that contains genes only found in a single strain. Some authors also refer to the cloud genome as "accessory genome" containing 'dispensable' genes present in a subset of the strains and strain-specific genes. Note that the use of the term 'dispensable' has been questioned, at least in plant genomes, as accessory genes play "an important role in genome evolution and in the complex interplay between the genome and the environment". The field of study of pangenomes is called pangenomics.

SOAP is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.

The 1000 Plant Transcriptomes Initiative (1KP) was an international research effort to establish the most detailed catalogue of genetic variation in plants. It was announced in 2008 and headed by Gane Ka-Shu Wong and Michael Deyholos of the University of Alberta. The project successfully sequenced the transcriptomes of 1000 different plant species by 2014; its final capstone products were published in 2019.

<span class="mw-page-title-main">Telluraves</span> Clade of birds

Telluraves is a recently defined clade of birds defined by their arboreality. Based on most recent genetic studies, the clade unites a variety of bird groups, including the australavians as well as the afroavians. They appear to be the sister group of the Phaethoquornithes.

<span class="mw-page-title-main">Li Jiayang</span> Chinese agronomist, Vice Minister of Agriculture (born 1956)

Li Jiayang is a Chinese agronomist and geneticist. He is Vice Minister of Agriculture in China and President of the Chinese Academy of Agricultural Sciences (CAAS). He is also Professor and Principal investigator at the Institute of Genetics and Development at the Chinese Academy of Sciences (CAS).

The Earth BioGenome Project (EBP) is an initiative that aims to sequence and catalog the genomes of all of Earth's currently described eukaryotic species over a period of ten years. The initiative would produce an open DNA database of biological information that provides a platform for scientific research and supports environmental and conservation initiatives. A scientific paper presenting the vision for the project was published in PNAS in April 2018, and the project officially launched November 1, 2018.

A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA fragments that are obtained from different types of sequencing technology.

Bat coronavirus RaTG13 is a SARS-like betacoronavirus identified in the droppings of the horseshoe bat Rhinolophus affinis. It was discovered in 2013 in bat droppings from a mining cave near the town of Tongguan in Mojiang county in Yunnan, China. In February 2020, it was identified as the closest known relative of SARS-CoV-2, the virus that causes COVID-19, sharing 96.1% nucleotide identity. However, in 2022, scientists found three closer matches in bats found 530 km south, in Feuang, Laos, designated as BANAL-52, BANAL-103 and BANAL-236.

RmYN02 is a bat-derived strain of Severe acute respiratory syndrome–related coronavirus. It was discovered in bat droppings collected between May and October 2019 from sites in Mengla County, Yunnan Province, China. It is the second-closest known relative of SARS-CoV-2, the virus strain that causes COVID-19, sharing 93.3% nucleotide identity at the scale of the complete virus genome. RmYN02 contains an insertion at the S1/S2 cleavage site in the spike protein, similar to SARS-CoV-2, suggesting that such insertion events can occur naturally.

RacCS203 is a bat-derived strain of severe acute respiratory syndrome–related coronavirus collected in acuminate horseshoe bats from sites in Thailand and sequenced by Lin-Fa Wang's team. It has 91.5% sequence similarity to SARS-CoV-2 and is most related to the RmYN02 strain. Its spike protein is closely related to RmYN02's spike, both highly divergent from SARS-CoV-2's spike.

Bat coronavirus RpYN06 is a SARS-like betacoronavirus that infects the horseshoe bat Rhinolophus pusillus. It is a close relative of SARS-CoV-2 with a 94.48% sequence identity.

LYRa11 is a SARS-like coronavirus (SL-COV) which was identified in 2011 in samples of intermediate horseshoe bats in Baoshan, Yunnan, China. The genome of this virus strain is 29805nt long, and the similarity to the whole genome sequence of SARS-CoV that caused the SARS outbreak is 91%. It was published in 2014. Like SARS-CoV and SARS-CoV-2, LYRa11 virus uses ACE2 as a receptor for infecting cells.

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