{"id":13973,"date":"2024-09-25T10:05:14","date_gmt":"2024-09-25T14:05:14","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13973"},"modified":"2024-09-27T12:28:15","modified_gmt":"2024-09-27T16:28:15","slug":"updated-terminology-reference-genome","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/25\/updated-terminology-reference-genome\/","title":{"rendered":"Updated Genomes Terminology! \u201cRepresentative Genome\u201d is Replaced with \u201cReference Genome\u201d"},"content":{"rendered":"<p><span data-contrast=\"none\">NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowly converged on the term reference to refer to both sets.\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">A genome is labeled reference if it is deemed to be the best available genome for the species based on assembly, annotation metrics (when available), and, in a small number of cases, curatorial review. The set of eukaryotic reference assemblies is updated continuously as new assemblies are submitted to <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=terminology-reference-genome-20240925\"><span data-contrast=\"none\">GenBank<\/span><\/a><span data-contrast=\"none\">. The set of prokaryotic references are recalculated three times a year.\u00a0<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><b><span data-contrast=\"none\">Important Note:<\/span><\/b><span data-contrast=\"none\"> Classification of \u201creference genome\u201d is separate from inclusion in <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=terminology-reference-genome-20240925\">RefSeq<\/a> \u2013 while genomes in RefSeq are preferentially used to pick the reference genome, a reference genome can also be chosen for species not included in RefSeq.\u00a0<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><!--more--><\/p>\n<h5><b><span data-contrast=\"none\">What\u2019s new?<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">The term &#8220;representative genome&#8221; is deprecated and replaced with &#8220;reference genome&#8221;<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">The terminology used in the files posted on our FTP site has been updated to reflect the change\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">The eutils search term \u201crepresentative&#8221; is discontinued\u00a0<\/span><\/li>\n<\/ul>\n<h5><b><span data-contrast=\"none\">Learn more<\/span><\/b><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">For more details, see our <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/v2\/policies-annotation\/genome-processing\/reference-selection\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=terminology-reference-genome-20240925\"><span data-contrast=\"none\">help documentation<\/span><\/a><span data-contrast=\"none\">.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"none\">Stay up to date\u202f<\/span><\/b><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">Follow us on social\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202fto keep up to date with RefSeq and other NCBI news.\u202f\u202f\u202f\u202f<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"none\">Questions?\u202f<\/span><\/b><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">We want to hear from you! If you have questions or would like to provide feedback, please reach out to us at\u202f<\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"none\">.\u202f\u202f\u202f<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowly converged on the term reference to refer to both sets.\u00a0\u00a0 A genome is labeled reference if it is deemed to be the best available genome &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/25\/updated-terminology-reference-genome\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Updated Genomes Terminology! \u201cRepresentative Genome\u201d is Replaced with \u201cReference Genome\u201d<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13977,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"Updated Genomes Terminology! \u201cRepresentative Genome\u201d is Replaced with \u201cReference Genome\u201d","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[1201719,693060836,69084386,27739816,693060689],"table_tags":[],"class_list":["post-13973","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-genbank","tag-ncbi-datasets","tag-reference-genome","tag-refseq","tag-representative-genome"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Updated Genomes Terminology! \u201cRepresentative Genome\u201d is Replaced with \u201cReference Genome\u201d - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/25\/updated-terminology-reference-genome\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Updated Genomes Terminology! \u201cRepresentative Genome\u201d is Replaced with \u201cReference Genome\u201d - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. 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We currently have a small set of genomes collectively called representatives and an even smaller set called references. 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