Ensembl Plants

<!DOCTYPE html> <html lang="en-gb"> <head> <title>Ensembl Plants</title> <link rel="stylesheet" type="text/css" media="all" href="/minified/c9c016e96d1f4c5385f8e1ba59443b47.css"/><link rel="stylesheet" type="text/css" media="all" href="/minified/866800a2d946647c0a02e85921121506.image.css"/> <link type="image/png" rel="icon" href="/i/ensembl-favicon.png" /> <link type="image/png" href="/apple-touch-icon.png" rel="apple-touch-icon" /> <link rel="search" href="//plants.ensembl.org/opensearch/all.xml" title="Ensembl (All)" type="application/opensearchdescription+xml" /> <meta name="description" content="Ensembl Plants is a genome-centric portal for plant species of scientific interest" /> <meta name="viewport" content="target-densitydpi=device-dpi, width=device-width, initial-scale=1.0, maximum-scale=2.0, user-scalable=yes" /> <script>var prefetch = [];</script> </head> <body data-pace="2" id="ensembl-webpage" class="ie ie7 ie67 no_tabs static"> <div id="min_width_container"> <div 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{"dataset":{"includedInDataCatalog":"http://.ensembl.org/#project","distribution":[{"description":"Alignments of resequencing data across the full taxonomic tree","contentURL":"https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/pan_ensembl/current/emf/ensembl-compara/homologies/","name":"Pan Comparative Genomics - EMF files","@type":"DataDownload","fileFormat":"emf"},{"description":"Alignments of resequencing data for Ensembl species","fileFormat":"emf","contentURL":"https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants//current/emf/ensembl-compara/homologies/","@type":"DataDownload","name":"Ensembl Plants Comparative Genomics - EMF files"}],"url":"/info/genome/compara","name":"Ensembl Plants Comparative Genomics Data","@type":"Dataset","keywords":"phylogenetics, evolution, homology, synteny","description":"Cross-genome resources and analyses at both the sequence level and the gene level"},"@id":"http://.ensembl.org/#project","@context":"http://schema.org","keywords":"genomics, bioinformatics, 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thaliana</option><option value="Oryza_sativa">Oryza sativa Japonica Group</option><option value="Triticum_aestivum">Triticum aestivum</option><option value="Hordeum_vulgare">Hordeum vulgare</option><option value="Zea_mays">Zea mays</option><option value="Physcomitrium_patens">Physcomitrium patens</option></optgroup><option value="" disabled="disabled">---</option><option value="Actinidia_chinensis">Actinidia chinensis</option><option value="Aegilops_tauschii">Aegilops tauschii</option><option value="Aegilops_umbellulata">Aegilops umbellulata</option><option value="Amborella_trichopoda">Amborella trichopoda</option><option value="Ananas_comosus">Ananas comosus</option><option value="Arabidopsis_halleri">Arabidopsis halleri</option><option value="Arabidopsis_lyrata">Arabidopsis lyrata</option><option value="Arabidopsis_thaliana">Arabidopsis thaliana</option><option value="Arabis_alpina">Arabis alpina</option><option value="Arachis_hypogaea">Arachis hypogaea</option><option value="Asparagus_officinalis">Asparagus officinalis</option><option value="Avena_sativa_OT3098">Avena sativa OT3098</option><option value="Avena_sativa_Sang">Avena sativa Sang</option><option value="Beta_vulgaris">Beta vulgaris</option><option value="Brachypodium_distachyon">Brachypodium distachyon</option><option value="Brassica_juncea">Brassica juncea</option><option value="Brassica_napus">Brassica napus</option><option value="Brassica_oleracea">Brassica oleracea</option><option value="Brassica_rapa">Brassica rapa</option><option value="Brassica_rapa_ro18">Brassica rapa R-o-18</option><option value="Brassica_rapa_z1">Brassica rapa Z1</option><option value="Cajanus_cajan">Cajanus cajan (pigeon pea) - GCA_000340665.1</option><option value="Camelina_sativa">Camelina sativa</option><option value="Cannabis_sativa_female">Cannabis sativa female</option><option value="Capsicum_annuum">Capsicum annuum</option><option value="Chara_braunii">Chara braunii</option><option value="Chenopodium_quinoa">Chenopodium quinoa</option><option value="Chlamydomonas_reinhardtii">Chlamydomonas reinhardtii</option><option value="Chondrus_crispus">Chondrus crispus</option><option value="Citrullus_lanatus">Citrullus lanatus</option><option value="Citrus_clementina">Citrus clementina</option><option value="Coffea_canephora">Coffea canephora</option><option value="Corchorus_capsularis">Corchorus capsularis</option><option value="Corylus_avellana">Corylus avellana</option><option value="Corymbia_citriodora">Corymbia citriodora</option><option value="Cucumis_melo">Cucumis melo</option><option value="Cucumis_sativus">Cucumis sativus</option><option value="Cyanidioschyzon_merolae">Cyanidioschyzon merolae</option><option value="Cynara_cardunculus">Cynara cardunculus</option><option value="Daucus_carota">Daucus carota</option><option value="Digitaria_exilis">Digitaria exilis</option><option value="Dioscorea_rotundata">Dioscorea rotundata</option><option value="Echinochloa_crusgalli">Echinochloa crus-galli</option><option value="Eragrostis_curvula">Eragrostis curvula</option><option value="Eragrostis_tef">Eragrostis tef</option><option value="Eucalyptus_grandis">Eucalyptus grandis</option><option value="Eutrema_salsugineum">Eutrema salsugineum</option><option value="Ficus_carica">Ficus carica</option><option value="Fraxinus_excelsior">Fraxinus excelsior</option><option value="Galdieria_sulphuraria">Galdieria sulphuraria</option><option value="Glycine_max">Glycine max</option><option value="Glycine_soja">Glycine soja (Wild soybean)</option><option value="Gossypium_raimondii">Gossypium raimondii</option><option value="Helianthus_annuus">Helianthus annuus</option><option value="Hordeum_vulgare">Hordeum vulgare</option><option value="Hordeum_vulgare_goldenpromise">Hordeum vulgare GoldenPromise</option><option value="Hordeum_vulgare_TRITEX">Hordeum vulgare TRITEX</option><option value="Ipomoea_triloba">Ipomoea triloba</option><option value="Juglans_regia">Juglans regia</option><option value="Kalanchoe_fedtschenkoi">Kalanchoe fedtschenkoi</option><option value="Lactuca_sativa">Lactuca sativa</option><option value="Lathyrus_sativus">Lathyrus sativus</option><option value="Leersia_perrieri">Leersia perrieri</option><option value="Lolium_perenne">Lolium perenne</option><option value="Lupinus_angustifolius">Lupinus angustifolius</option><option value="Malus_domestica_golden">Malus domestica Golden</option><option value="Manihot_esculenta">Manihot esculenta</option><option value="Marchantia_polymorpha">Marchantia polymorpha</option><option value="Medicago_truncatula">Medicago truncatula</option><option value="Musa_acuminata">Musa acuminata</option><option value="Nicotiana_attenuata">Nicotiana attenuata</option><option value="Nymphaea_colorata">Nymphaea colorata</option><option value="Olea_europaea">Olea europaea</option><option value="Olea_europaea_sylvestris">Olea europaea var. sylvestris</option><option value="Oryza_barthii">Oryza barthii</option><option value="Oryza_brachyantha">Oryza brachyantha</option><option value="Oryza_glaberrima">Oryza glaberrima</option><option value="Oryza_glumipatula">Oryza glumipatula</option><option value="Oryza_longistaminata">Oryza longistaminata</option><option value="Oryza_meridionalis">Oryza meridionalis</option><option value="Oryza_nivara">Oryza nivara</option><option value="Oryza_punctata">Oryza punctata</option><option value="Oryza_rufipogon">Oryza rufipogon</option><option value="Oryza_sativa_n22">Oryza sativa (circum-Aus1 var. N22)</option><option value="Oryza_sativa_natelboro">Oryza sativa (circum-Aus2 var. Natel Boro)</option><option value="Oryza_sativa_arc">Oryza sativa (circum-Basmati var. ARC 10497)</option><option value="Oryza_sativa_chaomeo">Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo)</option><option value="Oryza_sativa_azucena">Oryza sativa (Geng/Japonica-trop1 var. Azucena)</option><option value="Oryza_sativa_ketannangka">Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka)</option><option value="Oryza_sativa_zs97">Oryza sativa (Xian/Indica-1A var. Zhenshan 97)</option><option value="Oryza_sativa_ir64">Oryza sativa (Xian/Indica-1B1 var. IR64)</option><option value="Oryza_sativa_pr106">Oryza sativa (Xian/Indica-1B2 var. PR106)</option><option value="Oryza_sativa_gobolsailbalam">Oryza sativa (Xian/Indica-2A var. Gobol Sail)</option><option value="Oryza_sativa_larhamugad">Oryza sativa (Xian/Indica-2B var. Larha Mugad)</option><option value="Oryza_sativa_lima">Oryza sativa (Xian/Indica-3A var. Lima)</option><option value="Oryza_sativa_khaoyaiguang">Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang)</option><option value="Oryza_sativa_liuxu">Oryza sativa (Xian/Indica-3B2 var. Liu Xu)</option><option value="Oryza_sativa_mh63">Oryza sativa (Xian/Indica-adm var. Minghui 63)</option><option value="Oryza_indica">Oryza sativa Indica Group</option><option value="Oryza_sativa">Oryza sativa Japonica Group</option><option value="Ostreococcus_lucimarinus">Ostreococcus lucimarinus</option><option value="Panicum_hallii_fil2">Panicum hallii FIL2</option><option value="Panicum_hallii">Panicum hallii HAL2</option><option value="Papaver_somniferum">Papaver somniferum</option><option value="Phaseolus_vulgaris">Phaseolus vulgaris</option><option value="Physcomitrium_patens">Physcomitrium patens</option><option value="Pistacia_vera">Pistacia vera</option><option value="Pisum_sativum">Pisum sativum</option><option value="Populus_trichocarpa">Populus trichocarpa</option><option value="Prunus_avium">Prunus avium</option><option value="Prunus_dulcis">Prunus dulcis</option><option value="Prunus_persica">Prunus persica</option><option value="Quercus_lobata">Quercus lobata</option><option value="Quercus_suber">Quercus suber</option><option value="Rosa_chinensis">Rosa chinensis</option><option value="Saccharum_spontaneum">Saccharum spontaneum</option><option value="Secale_cereale">Secale cereale</option><option value="Selaginella_moellendorffii">Selaginella moellendorffii</option><option value="Sesamum_indicum">Sesamum indicum</option><option value="Setaria_italica">Setaria italica</option><option value="Setaria_viridis">Setaria viridis</option><option value="Solanum_lycopersicum">Solanum lycopersicum</option><option value="Solanum_tuberosum">Solanum tuberosum</option><option value="Solanum_tuberosum_RH8903916">Solanum tuberosum RH89-039-16</option><option value="Sorghum_bicolor">Sorghum bicolor</option><option value="Theobroma_cacao_criollo">Theobroma cacao Belizian Criollo B97-61/B2</option><option value="Theobroma_cacao">Theobroma cacao Matina 1-6</option><option value="Trifolium_pratense">Trifolium pratense</option><option value="Triticum_aestivum">Triticum aestivum</option><option value="Triticum_aestivum_arinalrfor">Triticum aestivum Arinalrfor</option><option value="Triticum_aestivum_cadenza">Triticum aestivum Cadenza</option><option value="Triticum_aestivum_claire">Triticum aestivum Claire</option><option value="Triticum_aestivum_jagger">Triticum aestivum Jagger</option><option value="Triticum_aestivum_julius">Triticum aestivum Julius</option><option value="Triticum_aestivum_kariega">Triticum aestivum Kariega</option><option value="Triticum_aestivum_lancer">Triticum aestivum Lancer</option><option value="Triticum_aestivum_landmark">Triticum aestivum Landmark</option><option value="Triticum_aestivum_mace">Triticum aestivum Mace</option><option value="Triticum_aestivum_norin61">Triticum aestivum Norin61</option><option value="Triticum_aestivum_paragon">Triticum aestivum Paragon</option><option value="Triticum_aestivum_refseqv2">Triticum aestivum Refseqv2</option><option value="Triticum_aestivum_renan">Triticum aestivum Renan</option><option value="Triticum_aestivum_robigus">Triticum aestivum Robigus</option><option value="Triticum_aestivum_stanley">Triticum aestivum Stanley</option><option value="Triticum_aestivum_mattis">Triticum aestivum Sy Mattis</option><option value="Triticum_aestivum_weebil">Triticum aestivum Weebill</option><option value="Triticum_dicoccoides">Triticum dicoccoides</option><option value="Triticum_spelta">Triticum spelta</option><option value="Triticum_timopheevii">Triticum timopheevii</option><option value="Triticum_turgidum">Triticum turgidum</option><option value="Triticum_urartu">Triticum urartu</option><option value="Vicia_faba">Vicia faba</option><option value="Vigna_angularis">Vigna angularis</option><option value="Vigna_radiata">Vigna radiata</option><option value="Vigna_unguiculata">Vigna unguiculata</option><option value="Vitis_vinifera">Vitis vinifera</option><option value="Zea_mays">Zea mays</option></select><label for="q">for</label></span><wbr></wbr><span class="inp-group"><input class="_string optional input query inactive ftext" name="q" type="text" id="q" size="30" value="" /><input value="Go" class="fbutton" type="submit" /></span><wbr></wbr></div><div class="ff-notes"><p class="search-example">e.g. <a class="nowrap" href="/Multi/Psychic?q=Carboxy*;site=ensemblunit">Carboxy*</a> or <a class="nowrap" href="/Multi/Psychic?q=chx28;site=ensemblunit">chx28</a></p></div></div></fieldset></form></div> </div> <div class="plain-box"> <div class="js_panel"> <input type="hidden" class="panel_type" value="SpeciesList" /> <div class="column_wrapper"><div class="static_all_species column-two"><h3>All genomes</h3> <p><select class="fselect _all_species"><option value="">-- Select a species --</option></select></p> <h3 class="space-above"></h3> <p><a href="/species.html">View full list of all species</a></p> </div><div class="column-two fave-genomes"><h3>Favourite genomes <a href="/Multi/Account/Login" class="_list_edit modal_link"><img src="/i/16/pencil.png" class="left-half-margin" title="Edit your favourites"></a></h3><div class="clear hidden reorder_species _species_sort_container"><p>For easy access to commonly used genomes, drag from the bottom list to the top one</p> <p><strong>Favourites</strong></p> <ul class="_favourites"></ul> <p><a href="#Done" class="button _list_done">Done</a> <a href="#Reset" class="button _list_reset">Restore default list</a></p> <p><strong>Other available species</strong></p> <ul class="_species"></ul> </div><div class="_species_fav_container species-list"> <div class="species-box-outer"> <div class="species-box"> <a href="/Arabidopsis_thaliana/Info/Index"><img src="/i/species/Arabidopsis_thaliana.png" alt="Arabidopsis_thaliana" title="Browse Arabidopsis_thaliana" class="badge-48"/></a> <a href="/Arabidopsis_thaliana/Info/Index" class="species-name">Arabidopsis thaliana</a> <div class="assembly">TAIR10</div> </div> </div> <div class="species-box-outer"> <div class="species-box"> <a href="/Oryza_sativa/Info/Index"><img src="/i/species/Oryza_sativa.png" alt="Oryza_sativa" title="Browse Oryza_sativa" class="badge-48"/></a> <a href="/Oryza_sativa/Info/Index" class="species-name">Oryza sativa Japonica Group</a> <div class="assembly">IRGSP-1.0</div> </div> </div> <div class="species-box-outer"> <div class="species-box"> <a href="/Triticum_aestivum/Info/Index"><img src="/i/species/Triticum_aestivum.png" alt="Triticum_aestivum" title="Browse Triticum_aestivum" class="badge-48"/></a> <a href="/Triticum_aestivum/Info/Index" class="species-name">Triticum aestivum</a> <div class="assembly">IWGSC</div> </div> </div> <div class="species-box-outer"> <div class="species-box"> <a href="/Hordeum_vulgare/Info/Index"><img src="/i/species/Hordeum_vulgare.png" alt="Hordeum_vulgare" title="Browse Hordeum_vulgare" class="badge-48"/></a> <a href="/Hordeum_vulgare/Info/Index" class="species-name">Hordeum vulgare</a> <div class="assembly">MorexV3_pseudomolecules_assembly</div> </div> </div> <div class="species-box-outer"> <div class="species-box"> <a href="/Zea_mays/Info/Index"><img src="/i/species/Zea_mays.png" alt="Zea_mays" title="Browse Zea_mays" class="badge-48"/></a> <a href="/Zea_mays/Info/Index" class="species-name">Zea mays</a> <div class="assembly">Zm-B73-REFERENCE-NAM-5.0</div> </div> </div> <div class="species-box-outer"> <div class="species-box"> <a href="/Physcomitrium_patens/Info/Index"><img src="/i/species/Physcomitrium_patens.png" alt="Physcomitrium_patens" title="Browse Physcomitrium_patens" class="badge-48"/></a> <a href="/Physcomitrium_patens/Info/Index" class="species-name">Physcomitrium patens</a> <div class="assembly">Phypa_V3</div> </div> </div></div><input type="hidden" name="fav_template" class="js_param" value=" <div class="species-box-outer"> <div class="species-box"> <a href="{{species.homepage}}"><img src="{{species.img}}" alt="{{species.name}}" title="Browse {{species.name}}" class="badge-48"/></a> <a href="{{species.homepage}}" class="species-name">{{species.common}}</a> <div class="assembly">{{species.assembly}}</div> </div> 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angularis","extra":"","assembly":"Vigan1.1"},{"strainspage":"","strain_type":"","homepage":"/Vigna_radiata/Info/Index","extra":"","common":"Vigna radiata","assembly":"Vradiata_ver6","group":"eudicotyledons","key":"Vigna_radiata","has_alt":0,"name":"Vigna_radiata","assembly_v":"Vradiata_ver6","straintitle":"Vigna radiata","favourite":0,"img":"/i/species/Vigna_radiata.png"},{"img":"/i/species/Vigna_unguiculata.png","name":"Vigna_unguiculata","assembly_v":"ASM411807v1","favourite":0,"straintitle":"Vigna unguiculata","group":"eudicotyledons","key":"Vigna_unguiculata","has_alt":0,"common":"Vigna unguiculata","extra":"","assembly":"ASM411807v1","homepage":"/Vigna_unguiculata/Info/Index","strain_type":"","strainspage":""},{"img":"/i/species/Vitis_vinifera.png","name":"Vitis_vinifera","assembly_v":"PN40024.v4","straintitle":"Vitis vinifera","favourite":0,"group":"eudicotyledons","key":"Vitis_vinifera","has_alt":0,"extra":"","common":"Vitis vinifera","assembly":"PN40024.v4","strain_type":"","strainspage":"","homepage":"/Vitis_vinifera/Info/Index"}]" class="js_param json" name="species_list" type="hidden" /><input type="hidden" class="js_param json" name="strains_list" value="[{"common":"Oryza sativa Japonica Group cultivars","name":"Oryza_sativa","homepage":"/Oryza_sativa/Info/Cultivars"},{"homepage":"/Triticum_aestivum/Info/Cultivars","name":"Triticum_aestivum","common":"Triticum aestivum cultivars"},{"common":"Hordeum vulgare cultivars","name":"Hordeum_vulgare","homepage":"/Hordeum_vulgare/Info/Cultivars"},{"homepage":"/Brassica_rapa_ro18/Info/Cultivars","name":"Brassica_rapa_ro18","common":"Brassica rapa R-o-18 cultivars"},{"homepage":"/Olea_europaea/Info/Varieties","common":"Olea europaea varieties","name":"Olea_europaea"},{"common":"Panicum hallii HAL2 ecotypes","name":"Panicum_hallii","homepage":"/Panicum_hallii/Info/Ecotypes"},{"name":"Solanum_tuberosum","common":"Solanum tuberosum cultivars","homepage":"/Solanum_tuberosum/Info/Cultivars"},{"homepage":"/Theobroma_cacao/Info/Cultivars","name":"Theobroma_cacao","common":"Theobroma cacao Matina 1-6 cultivars"}]" /><input type="hidden" name="ajax_refresh_url" class="js_param" value="Ajax/html_doc?db=core;module=GenomeList" /><input value="/Multi/Account/Favourites/Save" name="ajax_save_url" class="js_param" type="hidden" /><input type="hidden" class="js_param" name="display_limit" value="6" /><input class="js_param" name="fave_text" type="hidden" value="Favourite" /><input class="json js_param" name="taxon_labels" type="hidden" value="{}" /><input name="taxon_order" class="js_param json" type="hidden" value="["Liliopsida","eudicotyledons","Lycopodiophyta","Amborellales","Embryophyta","Streptophyta","Chlorophyta","Rhodophyta","Eukaryota"]" /></div></div> </div> </div> <div class="plain-box"><h2>What's New in Release 60</h2> <div class="info-box embedded-box float-right"> <h3>Did you know...?</h3> <p><a href="https://trackhubregistry.org/"><img alt="The Track Hub Registry" src="/img/thr-02.png" style="float:right; height:40px; margin-left:5px; margin-right:5px; width:40px" title="The Track Hub Registry" /></a> You can search the <a href="https://trackhubregistry.org">Track Hub Registry</a> to find public RNA-Seq studies aligned to plant genomes (<a href="https://www.ebi.ac.uk/fg/rnaseq/api/index.html#PerformingRNA-seqAnalysis">read more</a>).</p> </div> <ul> <li><p>New genomes</p> <ul> <li><p><a href="/Arachis_hypogaea">Arachis hypogaea</a> : assembly from <a href="http://www.insdc.org">INSDC</a> and is linked to the assembly accession <a href="https://www.ebi.ac.uk/ena/browser/view/GCA_003086295.3/">GCA_003086295.3</a> and annotation from <a href="https://www.peanutbase.org/genome/">International Peanut Genome Initiative</a>.</p></li> <li><p><a href="/Lathyrus_sativus">Lathyrus sativus</a> : assembly from <a href="http://www.insdc.org">INSDC</a> and is linked to the assembly accession <a href="https://www.ebi.ac.uk/ena/browser/view/GCA_963859935.3/">GCA_963859935.3</a> and annotation from <a href="https://www.jic.ac.uk/">John Innes Centre</a>.</p></li> <li><p><a href="/Triticum_timopheevii">Triticum timopheevii</a> : assembly from <a href="http://www.insdc.org">INSDC</a> and is linked to the assembly accession <a href="http://www.ebi.ac.uk/ena/data/view/GCA_963921465.1">GCA_963921465.1</a> and annotation from <a href="https://www.nottingham.ac.uk/">The University of Nottingham</a>.</p></li> </ul></li> <li><p>Updated genomes</p> <ul> <li><p><a href="/Brassica_rapa_z1">Brassica rapa Z1</a> : assembly from <a href="http://www.insdc.org">INSDC</a> and is linked to the assembly accession <a href="http://www.ebi.ac.uk/ena/data/view/GCA_900412535.3">GCA_900412535.3</a> and annotation from <a href="https://www.genoscope.cns.fr/externe/plants/">Genoscope</a>. It has been added as a <a href="https://plants.ensembl.org/Brassica_rapa_ro18/Info/Cultivars?db=core">cultivar</a>. </p></li> <li><p><a href="/Marchantia_polymorpha">Marchantia polymorpha</a> : assembly from <a href="http://www.insdc.org">INSDC</a> and is linked to the assembly accession <a href="http://www.ebi.ac.uk/ena/data/view/GCA_039105155.1">GCA_039105155.1</a> and annotation from <a href="https://www.nig.ac.jp/nig/">National Institute of Genetics</a>.</p></li> <li><p><a href="/Triticum_aestivum_Paragon">Triticum aestivum Paragon</a> : assembly from <a href="http://www.insdc.org">INSDC</a> and is linked to the assembly accession <a href="https://www.ebi.ac.uk/ena/browser/view/GCA_949126075.1">GCA_949126075.1</a> and annotation from <a href="https://opendata.earlham.ac.uk/">Earlham Institute</a>.</p></li> </ul></li> </ul> <p>Check which features are supported on each species <a href="/species.html">here</a>; if you would like to request a new species please email <a href="http://plants.ensembl.org/Help/Contact">Helpdesk</a>.</p> <div id="rapidbox"> <h2>Ensembl Rapid Release</h2> <p><b>New genome assemblies are now being released to the <a target="_blank" href="http://beta.ensembl.org">Ensembl Beta site</a> </b>.</p> <p>All Rapid Release data, including release 65, has been uploaded into the new Ensembl Beta site.</p> <p>The Ensembl Rapid Release website will remain active for the foreseeable future, however, the data and species set will no longer be updated.</p> <p class="right">Find out more on our <a href="https://www.ensembl.info/2024/11/14/we-will-be-freezing-ensembl-rapid-release/" target="_blank">blog</a></p> </div> </div> </div> </div> <div class="column-two"> <div class="column-padding no-right-margin"> <div class="plain-box"> <h2 id="wheatassemblies">Wheat assemblies</h2> <p>Ensembl Plants hosts the <a href="http://plants.ensembl.org/Wheat">RefSeq v1.0 assembly</a> from the IWGSC, including:</p> <ul> <li>The IWGSC RefSeq v1.1 gene annotation, with links to <a href="http://www.wheat-expression.com">wheat expression browser</a> and <a href="https://knetminer.rothamsted.ac.uk/Triticum_aestivum/">KnetMiner</a> </li> <li><a href="/Triticum_aestivum/Info/Strains?db=core">17 wheat cultivars</a> from the <a href="http://www.10wheatgenomes.com">10+ genome project</a> and other sources including comparative analysis across the different lines </li> <li>~90 million variants from the <a href="https://www.jic.ac.uk/blog/the-a-e-watkins-landrace-collection-of-bread-wheat-who-was-ae-watkins/">Watkins Landrace Wheat Collection</a> </li> <li>Axiom 35K, 820K SNP arrays from <a href="https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/index.php">CerealsDB</a>, including QTL links in selected cases and Linkage Disequilibrium display - see QTL example <a href="https://plants.ensembl.org/Triticum_aestivum/Variation/Explore?r=5A:438266461-438267461;v=BA00617086;vdb=variation;vf=264386">here</a>. 820K variants have been lifted over to the chromosomal level 10+ wheat cultivars </li> <li>EMS-induced mutations from sequenced TILLING populations of Cadenza (coding regions) and Kronos (coding regions and promoters) </li> <li>Inter-Homeologous Variants (IHVs) between the A, B and D genome components </li> <li>Chromosome specific KASP markers from the Nottingham BBSRC Wheat Research Centre </li> <li>Whole genome alignments to rice, brachypodium and barley </li> <li>Polyploid view enabled, allowing users to view alignments among multiple wheat components <a href="http://plants.ensembl.org/Triticum_aestivum/Location/MultiPolyploid?db=core;g=TraesCS3D02G273600;r=3D:379535906-379539827;r1=3B:495135630-495139551:1;r2=3A:503751489-503755410:1;s1=Triticum_aestivum--3B;s2=Triticum_aestivum--3A">simultaneously</a> </li> <li>Durum wheat 35K, 90K, 820K and TaBW280K variants </li> <li>Chromosome and centromere data can be viewed <a href="/Triticum_aestivum/Location/Genome">here</a> </li> <li><a href="https://alphafold.ebi.ac.uk/">AlphaFold</a> protein predictions have been added to all transcripts - see an example <a href="http://plants.ensembl.org/Triticum_aestivum/Transcript/AFDB?db=core;g=TraesCS3D02G273600;r=3D:379535906-379539827;t=TraesCS3D02G273600.1">here</a> </li> </ul> </div> <div class="plain-box"> <h2 id="archivesites">Archive sites</h2> <p>Archive of release 59 of EnsemblPlants: <a href="https://eg59-plants.ensembl.org">eg59-plants.ensembl.org</a> (May 2024)</p> <p>Archive of release 56 of EnsemblPlants: <a href="https://eg56-plants.ensembl.org">eg56-plants.ensembl.org</a> (Feb 2023)</p> <p>Archive of release 52 of EnsemblPlants: <a href="https://eg52-plants.ensembl.org">eg52-plants.ensembl.org</a> (Dec 2021)</p> <p>Archive of release 49 of EnsemblPlants: <a href="https://eg49-plants.ensembl.org">eg49-plants.ensembl.org</a> (Dec 2020)</p> <p>Archive of release 45 of EnsemblPlants: <a href="https://eg45-plants.ensembl.org">eg45-plants.ensembl.org</a> (Sep 2019)</p> </div> <div class="plain-box"> <h3 id="funding">Funding</h3> <p>Ensembl Plants datasets are constructed in a direct collaboration with the <a href="http://www.gramene.org">Gramene</a> resource, funded by the United States <a href="http://www.nsf.gov/">National Science Foundation</a> <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=1127112">award 1127112</a>. Read <a href="/info/about/collaborations/gramene.html">more</a> about our collaboration with Gramene.</p> <p class="rtecenter"><a href="http://www.gramene.org/"><img alt="Gramene logo" src="/img/gramene_logo.png" style="height:60px; width:150px" /></a></p> <p>The development of resources for wheat is funded by the BBSRC-funded <a href="https://www.jic.ac.uk/research/designing-future-wheat/">Designing Future Wheat ISP</a> and <a href="https://gtr.ukri.org/projects?ref=BB%2FT015691%2F1">PanOryza</a> grants.</p> <p class="rtecenter"><a href="http://www.bbsrc.ac.uk/home/home.aspx"><img alt="BBSRC logo" src="/img/bbsrc.png" style="height:60px" /></a></p> <p>ELIXIR implementation study <a href="https://elixir-europe.org/about-us/commissioned-services/fondue">FONDUE - FAIR-ification of Plant Genotyping Data and its linking to Phenotyping using ELIXIR Platforms</a>.</p> <h3 id="pastfunding">Past Funding</h3> <p><a href="http://transplantdb.eu">transPLANT</a>, funded by the <a href="http://ec.europa.eu/index_en.htm">European Commission</a> within its <a href="http://cordis.europa.eu/fp7/home_en.html">7th Framework Programme</a>, under the thematic area "Infrastructures", contract number <a href="https://cordis.europa.eu/project/id/283496">283496</a>.</p> <p class="rtecenter"><a href="http://transplantdb.eu/"><img alt="transPLANT logo" src="/img/transPLANT_logo_small.jpg" style="height:80px; vertical-align:middle" /></a> <img alt="The European flag" src="/img/flag_yellow_low.jpg" style="height:60px; vertical-align:middle; width:88px" /></p> <p>BBSRC funding for wheat (<a href="http://www.wheatgenome.org.uk/">Triticeae Genomics For Sustainable Agriculture</a>) and barley (<a href="http://www.barleygenome.org.uk">UK barley genome sequencing project</a>).</p> <p>ELIXIR implementation study <a href="https://elixir-europe.org/about-us/commissioned-services/apple-genomic-information">Apple as a Model for Genomic Information Exchange</a>.</p> </div> <div class="plain-box"> <p><a href="http://ensemblgenomes.org/">Ensembl Genomes</a> is developed by <a href="http://www.ebi.ac.uk">EMBL-EBI</a> and is powered by the <a href="http://www.ensembl.org">Ensembl</a> software system for the analysis and visualisation of genomic data. 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