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By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <div id="content" class="site-content" role="main" itemscope itemtype="http://schema.org/Article"> <article id="post-15172" class="post-15172 post type-post status-publish format-standard hentry category-01-release tag-assembly tag-ensembl tag-ensembl-111 tag-ensembl-genomes tag-ensembl-genomes-58 tag-grch37 tag-metazoa tag-plants tag-plugin tag-variation tag-vep"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Ensembl 111 has been released!</h1> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/01/11/ensembl-111-has-been-released/" rel="bookmark"><time class="entry-date published" datetime="2024-01-11T13:55:14+00:00" itemprop="datepublished">11th January 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/bmoore/" rel="author" itemprop="url"><span itemprop="name">Ben (Outreach)</span></a></span><span class="sep">·</span><span class="comments-link"><a href="https://www.ensembl.info/2024/01/11/ensembl-111-has-been-released/#comments" itemprop="discussionUrl">6 Comments</a></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>We are pleased to announce the release of Ensembl 111, and the corresponding release of Ensembl Genomes 58 featuring a range of new Ensembl VEP plugins and tonnes of new and updated agricultural, fish, plant and metazoa species!</p> <p>Genome assemblies and annotation for many new species are also being continuously added to the <a href="https://rapid.ensembl.org/index.html" target="_blank" rel="noreferrer noopener">Ensembl Rapid Release genome browser</a>.</p> <span id="more-15172"></span> <h2 class="wp-block-heading">New Ensembl VEP plugins</h2> <p>We have added a whole host of new Ensembl <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#plugins_existing" target="_blank" rel="noreferrer noopener">VEP plugins</a> that provide additional variant annotation from a range of sources: </p> <p>The <a href="https://www.opentargets.org/" target="_blank" rel="noreferrer noopener">Open Targets</a> Genetics team uses a <a href="https://genetics-docs.opentargets.org/our-approach/prioritising-causal-genes-at-gwas-loci-l2g" target="_blank" rel="noreferrer noopener">Locus to Gene</a> (L2G) model to prioritise likely causal genes from published GWAS trait-associated loci. The OpenTargets plugin integrates these results by variant and will be available through the Ensembl VEP web interface, command-line and REST platforms. The web interface links to variant-specific pages in the Open Targets portal for further information.</p> <p><a href="https://fenglab.chpc.utah.edu/BayesDel/BayesDel.html" target="_blank" rel="noreferrer noopener">BayesDel</a> is a deleteriousness meta-score for both coding and non-coding variants. The BayesDel plugin integrates precalculated scores into Ensembl VEP and will initially be available through the command-line interface only.</p> <p><a href="https://www.sciencedirect.com/science/article/pii/S0002929721003207" target="_blank" rel="noreferrer noopener">Varity</a> predicts the pathogenicity of rare human missense variants. The Varity plugin will initially be available for Ensembl VEP command-line platform only.</p> <p>The DosageSensitivity plugin reports when a variant overlaps a dosage sensitive gene, as identified by <a href="https://doi.org/10.1016/j.cell.2022.06.036" target="_blank" rel="noreferrer noopener">Collins et al</a>. This plugin will initially be available through the Ensembl VEP command-line platform only.</p> <p>DeepMind’s <a href="https://www.nature.com/articles/s41592-021-01252-x" target="_blank" rel="noreferrer noopener">Enformer</a> deep learning architecture predicts variant effects on gene expression. The Enformer  plugin integrates precalculated scores and will initially be available through the Ensembl VEP command-line and REST platforms, with integration into the web interface planned for Ensembl 112.</p> <p>The deNovo plugin is designed to be used to annotate a VCF when pedigree information is available (in a .ped file). It will highlight when a variant (or ref) allele has arisen <em>de novo</em>. This plugin is currently only available on the command-line platform.</p> <p><a href="https://www.nature.com/articles/s41588-022-01293-8" target="_blank" rel="noreferrer noopener">SpliceVault</a> is a new VEP plugin that predicts exon-skipping events and activated cryptic splice sites based on the most common mis-splicing events. This plugin is currently only available on the command-line platform.</p> <h2 class="wp-block-heading">Human variation data update</h2> <p>The <a href="https://www.ensembl.org/info/genome/variation/species/sources_documentation.html" target="_blank" rel="noreferrer noopener">human variation data</a> available in Ensembl has been updated to include <a href="https://www.ncbi.nlm.nih.gov/snp/" target="_blank" rel="noreferrer noopener">dbSNP156</a>, which represents over 1 BILLION(!) individual variants.</p> <h2 class="wp-block-heading">GRCh37 update </h2> <p>The annotation on the <a href="https://grch37.ensembl.org/index.html" target="_blank" rel="noreferrer noopener">human GRCh37 genome assembly</a> has been updated to include dbSNP156 variants, the latest data from all variant and phenotype association sources including ClinVar, OMIM and the NHGRI-EBI GWAS Catalog, updated regulatory annotation and RefSeq data. The updated reference data will also be available in the Ensembl VEP cache, web tool and REST API.</p> <h2 class="wp-block-heading">New vertebrate genome assemblies and annotation</h2> <ul> <li>Assembly update for <a href="https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index">Sheep</a> (<em>Ovis aries</em>) reference – GCA_016772045.1 (ARS-UI_Ramb_v2.0) </li> <li>Assembly update for <a href="https://www.ensembl.org/Bos_taurus/Info/Index" target="_blank" rel="noreferrer noopener">Cattle</a> (<em>Bos taurus</em>) reference – GCA_002263795.3 (ARS-UCD1.3)</li> </ul> <ul> <li>New regulatory annotation for <a href="https://www.ensembl.org/Cyprinus_carpio_carpio/Info/Index" target="_blank" rel="noreferrer noopener">common carp</a> and <a href="https://www.ensembl.org/Oncorhynchus_mykiss/Info/Index" target="_blank" rel="noreferrer noopener">rainbow trout</a></li> <li>Updated regulatory annotation, including enhancers, for <a href="https://www.ensembl.org/Sus_scrofa/Info/Index" target="_blank" rel="noreferrer noopener">pig</a> and <a href="https://www.ensembl.org/Gallus_gallus/Info/Index" target="_blank" rel="noreferrer noopener">chicken</a>, <a href="https://www.ensembl.org/Salmo_salar/Info/Index" target="_blank" rel="noreferrer noopener">Atlantic salmon</a>, <a href="https://www.ensembl.org/Dicentrarchus_labrax/Info/Index">European seabass </a>and <a href="https://www.ensembl.org/Scophthalmus_maximus/Info/Index">turbot</a></li> </ul> <h2 class="wp-block-heading">New species</h2> <h3 class="wp-block-heading">Plants</h3> <p><a href="https://plants.ensembl.org/Glycine_soja/Info/Index">Wild soybean</a><em> (Glycine soja)</em> – GCA_004193775.2</p> <h3 class="wp-block-heading">Metazoa</h3> <p><a href="https://metazoa.ensembl.org/Adelges_cooleyi_gca023614345v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Spruce gall adelgid</a> <em>(Adelges cooleyi)</em> – GCA_023614345.1</p> <p><a href="https://metazoa.ensembl.org/Aethina_tumida_gca024364675v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Small hive beetle</a> <em>(Aethina tumida)</em> – GCA_024364675.1</p> <p><a href="https://metazoa.ensembl.org/Amblyteles_armatorius_gca933228735v1/Info/Index">Parasitic wasp</a> <em>(Amblyteles armatorius)</em> – GCA_933228735.1</p> <p><a href="https://metazoa.ensembl.org/Ancistrocerus_nigricornis_gca916049575v1/Info/Index" target="_blank" rel="noreferrer noopener">Potter wasp</a> <em>(Ancistrocerus nigricornis)</em> – GCA_916049575.1</p> <p><a href="https://metazoa.ensembl.org/Bombus_huntii_gca024542735v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Hunt’s bumblebee</a> <em>(Bombus huntii</em>) – GCA_024542735.1</p> <p><a href="https://metazoa.ensembl.org/Bombus_vancouverensis_gca011952275v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Montane Bumble Bee</a> <em>(Bombus vancouverensis nearcticus</em>) – GCA_011952275.1</p> <p><a href="https://metazoa.ensembl.org/Cataglyphis_hispanica_gca021464435v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Desert ant</a> <em>(Cataglyphis hispanica</em>) – GCA_021464435.1</p> <p><a href="https://metazoa.ensembl.org/Crassostrea_angulata_gca025612915v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Portuguese oyster</a><em> (Crassostrea angulata) –</em> GCA_025612915.2</p> <p><a href="https://metazoa.ensembl.org/Cryptotermes_secundus_gca002891405v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Drywood termite</a> <em>(Cryptotermes secundus) –</em> GCA_002891405.2</p> <p><a href="https://metazoa.ensembl.org/Daktulosphaira_vitifoliae_gca025091365v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Grape phylloxera</a> <em>(Daktulosphaira vitifoliae) –</em> GCA_025091365.1</p> <p><a href="https://metazoa.ensembl.org/Dreissena_polymorpha_gca020536995v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Zebra mussel</a><em> (Dreissena polymorpha) –</em> GCA_020536995.1</p> <p><a href="https://metazoa.ensembl.org/Glyphotaelius_pellucidus_gca936435175v1/Info/Index">Caddisflies</a> <em>(Glyphotaelius pellucidus) –</em> GCA_936435175.1</p> <p><a href="https://metazoa.ensembl.org/Ichneumon_xanthorius_gca917499995v1/Info/Index" target="_blank" rel="noreferrer noopener">Ichneumon wasp</a> <em>(Ichneumon xanthorius)</em> – GCA_917499995.1</p> <p><a href="https://metazoa.ensembl.org/Limnephilus_lunatus_gca917563855v2/Info/Index" target="_blank" rel="noreferrer noopener">Caddisflies</a> <em>(Limnephilus lunatus) –</em> GCA_917563855.2</p> <p><a href="https://metazoa.ensembl.org/Limnephilus_marmoratus_gca917880885v1/Info/Index" target="_blank" rel="noreferrer noopener">Caddisflies</a> <em>(Limnephilus marmoratus) –</em> GCA_917880885.1</p> <p><a href="https://metazoa.ensembl.org/Limnephilus_rhombicus_gca929108145v2/Info/Index" target="_blank" rel="noreferrer noopener">Caddisflies</a> <em>(Limnephilus rhombicus) –</em> GCA_929108145.2</p> <p><a href="https://metazoa.ensembl.org/Limnoperna_fortunei_gca944474755v1/Info/Index" target="_blank" rel="noreferrer noopener">Golden mussel</a> <em>(Limnoperna fortunei</em>) – GCA_944474755.1</p> <p><a href="https://metazoa.ensembl.org/Lineus_longissimus_gca910592395v2/Info/Index" target="_blank" rel="noreferrer noopener">Bootlace worm</a> <em>(Lineus longissimus) –</em> GCA_910592395.2)</p> <p><a href="https://metazoa.ensembl.org/Macrosteles_quadrilineatus_gca028750875v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Aster leafhopper</a> <em>(Macrosteles quadrilineatus) –</em> GCA_028750875.1</p> <p><a href="https://metazoa.ensembl.org/Mya_arenaria_gca026914265v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Soft-shell clam</a> <em>(Mya arenaria) –</em> GCA_026914265.1</p> <p><a href="https://metazoa.ensembl.org/Oppia_nitens_gca028296485v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Oribatid soil mite</a> <em>(Oppia nitens) –</em> GCA_028296485.1</p> <p><a href="https://metazoa.ensembl.org/Ostrea_edulis_gca023158985v1rs/Info/Index" target="_blank" rel="noreferrer noopener">European flat oyster</a> <em>(Ostrea edulis) –</em> GCA_023158985.1</p> <p><a href="https://metazoa.ensembl.org/Panonychus_citri_gca014898815v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Citrus red mite</a> <em>(Panonychus citri) –</em> GCA_014898815.1</p> <p><a href="https://metazoa.ensembl.org/Patella_pellucida_gca917208275v1/Info/Index" target="_blank" rel="noreferrer noopener">Blue-rayed limpet</a><em> (Patella pellucida) –</em> GCA_917208275.1</p> <p><a href="https://metazoa.ensembl.org/Patella_vulgata_gca932274485v1/Info/Index" target="_blank" rel="noreferrer noopener">Common limpet</a> <em>(Patella vulgata) –</em> GCA_932274485.1</p> <p><a href="https://metazoa.ensembl.org/Schistocerca_cancellata_gca023864275v2rs/Info/Index" target="_blank" rel="noreferrer noopener">South American locust</a> <em>(Schistocerca cancellata) –</em> GCA_023864275.2</p> <p><a href="https://metazoa.ensembl.org/Schistocerca_gregaria_gca023897955v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Grasshoppers</a> <em>(Schistocerca gregaria) –</em> GCA_023897955.2</p> <p><a href="https://metazoa.ensembl.org/Schistocerca_nitens_gca023898315v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Vagrant locust</a> <em>(Schistocerca nitens) –</em> GCA_023898315.2</p> <p><a href="https://metazoa.ensembl.org/Schistocerca_piceifrons_gca021461385v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Central American locust</a> <em>(Schistocerca piceifrons) –</em> GCA_021461385.2</p> <p><a href="https://metazoa.ensembl.org/Schistocerca_serialis_gca023864345v3rs/Info/Index" target="_blank" rel="noreferrer noopener">Grasshoppers</a> <em>(Schistocerca serialis cubense) –</em> GCA_023864345.3</p> <p><a href="https://metazoa.ensembl.org/Varroa_jacobsoni_gca002532875v1rs/Info/Index" target="_blank" rel="noreferrer noopener">Varroa mite</a> <em>(Varroa jacobsoni) –</em> GCA_002532875.1</p> <h2 class="wp-block-heading">Other new assemblies and annotation</h2> <h3 class="wp-block-heading">Plants</h3> <p><a href="https://plants.ensembl.org/Quercus_suber/Info/Index" target="_blank" rel="noreferrer noopener">Cork oak</a> <em>(Quercus suber)</em> </p> <h3 class="wp-block-heading">Metazoa</h3> <p><a href="https://metazoa.ensembl.org/Dermacentor_silvarum_gca013339745v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Dermacentor silvarum</a> (Tick) assembly updated to GCA_013339745.2 </p> <p><a href="https://metazoa.ensembl.org/Rhipicephalus_sanguineus_gca013339695v2rs/Info/Index" target="_blank" rel="noreferrer noopener">Rhipicephalus sanguineus</a> (Tick) assembly updated to GCA_013339695.2</p> <h2 class="wp-block-heading">Removed assemblies</h2> <h3 class="wp-block-heading">Metazoa</h3> <p>Sand fly <em>(Phlebotomus perniciosus)</em> – older GCA_918844115.1</p> <p>Pea aphid <em>(Acyrthosiphon pisum)</em> – older GCA_005508785.1 </p> <p>Demosponge <em>(Amphimedon queenslandica)</em> – older GCA_000090795.1 </p> <p>Lamp shell <em>(Lingula anatina)</em> – older GCA_001039355.1 </p> <p>Tick (<em>Dermacentor silvarum</em>) – older GCA_013339745.1</p> <h2 class="wp-block-heading">Other updates and highlights</h2> <ul> <li>Transcript length to be added to the output of the REST lookup endpoint, when expand=1</li> <li>Retirement of Ensembl 93 and 94 archives</li> </ul> </div> <div class="tags-links"><a href="https://www.ensembl.info/tag/assembly/" rel="tag">assembly</a> <a href="https://www.ensembl.info/tag/ensembl/" rel="tag">Ensembl</a> <a href="https://www.ensembl.info/tag/ensembl-111/" rel="tag">Ensembl 111</a> <a href="https://www.ensembl.info/tag/ensembl-genomes/" rel="tag">Ensembl Genomes</a> <a href="https://www.ensembl.info/tag/ensembl-genomes-58/" rel="tag">Ensembl Genomes 58</a> <a href="https://www.ensembl.info/tag/grch37/" rel="tag">GRCh37</a> <a href="https://www.ensembl.info/tag/metazoa/" rel="tag">Metazoa</a> <a href="https://www.ensembl.info/tag/plants/" rel="tag">Plants</a> <a href="https://www.ensembl.info/tag/plugin/" rel="tag">plugin</a> <a href="https://www.ensembl.info/tag/variation/" rel="tag">variation</a> <a href="https://www.ensembl.info/tag/vep/" rel="tag">VEP</a></div></article> <nav class="navigation post-navigation" aria-label="Posts"> <h2 class="screen-reader-text">Post navigation</h2> <div class="nav-links"><div class="nav-previous"><a href="https://www.ensembl.info/2024/01/03/downtime-of-ensembl-tools-4/" rel="prev"><span class="meta-nav" aria-hidden="true">Previous</span> <span class="screen-reader-text">Previous post:</span> <span class="post-title">Downtime of Ensembl tools</span></a></div><div class="nav-next"><a href="https://www.ensembl.info/2024/01/18/downtime-of-the-ensembl-search-and-asia-mirror/" rel="next"><span class="meta-nav" aria-hidden="true">Next</span> <span class="screen-reader-text">Next 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