{"id":10430,"date":"2023-01-06T12:54:54","date_gmt":"2023-01-06T17:54:54","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=10430"},"modified":"2023-01-06T14:56:53","modified_gmt":"2023-01-06T19:56:53","slug":"bacterial-archaeal-reference-genomes","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/","title":{"rendered":"Updated bacterial and archaeal reference genomes collection now available!"},"content":{"rendered":"<p>An updated\u00a0<a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly\/?term=%28Bacteria%5Borgn%5D+OR+Archaea%5Borgn%5D%29+AND+%28reference_genome%5Bfilter%5D+OR+representative_genome%5Bfilter%5D%29&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20230106\" target=\"_blank\" rel=\"nofollow noopener\">bacterial and archaeal reference genome collection<\/a>\u00a0is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for\u00a0<em>E. coli<\/em>\u00a0for which two assemblies were selected as reference.<\/p>\n<p>A total of 497 species are included in this collection for the first time. In addition, comparing to the <a class=\"external-link\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20230106\" target=\"_blank\" rel=\"nofollow noopener\">October 2022 set<\/a>, 174 species are represented by a better assembly and 15 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment. The criteria for selecting one assembly for a given species from all assemblies available in RefSeq for the species include assembly contiguity and completeness and quality of the RefSeq annotation. See the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/about\/prokaryotes\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20230106#representative_genomes\">documentation<\/a> for details.<\/p>\n<p>We have updated the <a class=\"external-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20230106\" target=\"_blank\" rel=\"nofollow noopener\">nucleotide BLAST RefSeq reference genomes database<\/a>\u00a0(fourth in the menu) as well as the database on the\u00a0<a class=\"external-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=MicrobialGenomes&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20230106\" target=\"_blank\" rel=\"nofollow noopener\">Microbial Nucleotide BLAST page<\/a>\u00a0to reflect these changes. You can also run\u00a0<a class=\"external-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&amp;PAGE=Proteins&amp;PROGRAM=blastp&amp;DATABASE=refseq_select_prot&amp;BLAST_PROGRAMS=blastp\" target=\"_blank\" rel=\"nofollow noopener\">BLAST searches against the proteins annotated on these reference genomes<\/a> (RefSeq Select proteins database, second in the menu).<\/p>\n","protected":false},"excerpt":{"rendered":"<p>An updated\u00a0bacterial and archaeal reference genome collection\u00a0is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for\u00a0E. coli\u00a0for which two assemblies were selected as reference. A total of 497 species are included in this collection for the first time. &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Updated bacterial and archaeal reference genomes collection now available!<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":10443,"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 bacterial and archaeal representative genomes collection now available!","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":[77187,34457,53114734,576953096,27739816],"table_tags":[],"class_list":["post-10430","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-taxonomy","tag-blastn","tag-prokaryotic-genome-annotation","tag-refseq"],"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 bacterial and archaeal reference genomes collection now available! - 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\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Updated bacterial and archaeal reference genomes collection now available! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"An updated\u00a0bacterial and archaeal reference genome collection\u00a0is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for\u00a0E. coli\u00a0for which two assemblies were selected as reference. A total of 497 species are included in this collection for the first time. &hellip; Continue reading Updated bacterial and archaeal reference genomes collection now available! &rarr;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\" \/>\n<meta property=\"og:site_name\" content=\"NCBI Insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/ncbi.nlm\" \/>\n<meta property=\"article:published_time\" content=\"2023-01-06T17:54:54+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-01-06T19:56:53+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1100\" \/>\n\t<meta property=\"og:image:height\" content=\"575\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"NCBI Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@NCBI\" \/>\n<meta name=\"twitter:site\" content=\"@NCBI\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"NCBI Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Updated bacterial and archaeal reference genomes collection now available!\",\"datePublished\":\"2023-01-06T17:54:54+00:00\",\"dateModified\":\"2023-01-06T19:56:53+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\"},\"wordCount\":181,\"commentCount\":1,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Basic Local Alignment Search Tool (BLAST)\",\"NCBI Taxonomy\",\"Nucleotide BLAST (blastn)\",\"Prokaryotic genome annotation\",\"RefSeq\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\",\"name\":\"Updated bacterial and archaeal reference genomes collection now available! - NCBI Insights\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1\",\"datePublished\":\"2023-01-06T17:54:54+00:00\",\"dateModified\":\"2023-01-06T19:56:53+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1\",\"width\":1100,\"height\":575,\"caption\":\"Colorful prokaryotic organisms in the background. Text says: Prokaryotic Reference Genomes Collection Update\"},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Updated bacterial and archaeal reference genomes collection now available!\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/\",\"name\":\"National Center for Biotechnology Information\",\"description\":\"News about NCBI resources and events\",\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\",\"name\":\"National Center for Biotechnology Information\",\"alternateName\":\"NCBI\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/03\/nih-nlm-ncbi-two-color.png?fit=6374%2C760&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/03\/nih-nlm-ncbi-two-color.png?fit=6374%2C760&ssl=1\",\"width\":6374,\"height\":760,\"caption\":\"National Center for Biotechnology Information\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/www.facebook.com\/ncbi.nlm\",\"https:\/\/x.com\/NCBI\",\"https:\/\/www.linkedin.com\/company\/ncbinlm\/\"]},{\"@type\":\"Person\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\",\"name\":\"NCBI Staff\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/f706d65e16bb6bb171b72b4b26f66276?s=96&d=identicon&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/f706d65e16bb6bb171b72b4b26f66276?s=96&d=identicon&r=g\",\"caption\":\"NCBI Staff\"},\"description\":\"The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology.\",\"sameAs\":[\"http:\/\/ncbiinsights.wordpress.com\"],\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/author\/ncbiinsights\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Updated bacterial and archaeal reference genomes collection now available! - NCBI Insights","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/","og_locale":"en_US","og_type":"article","og_title":"Updated bacterial and archaeal reference genomes collection now available! - NCBI Insights","og_description":"An updated\u00a0bacterial and archaeal reference genome collection\u00a0is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for\u00a0E. coli\u00a0for which two assemblies were selected as reference. A total of 497 species are included in this collection for the first time. &hellip; Continue reading Updated bacterial and archaeal reference genomes collection now available! &rarr;","og_url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/","og_site_name":"NCBI Insights","article_publisher":"https:\/\/www.facebook.com\/ncbi.nlm","article_published_time":"2023-01-06T17:54:54+00:00","article_modified_time":"2023-01-06T19:56:53+00:00","og_image":[{"width":1100,"height":575,"url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png","type":"image\/png"}],"author":"NCBI Staff","twitter_card":"summary_large_image","twitter_creator":"@NCBI","twitter_site":"@NCBI","twitter_misc":{"Written by":"NCBI Staff","Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#article","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/"},"author":{"name":"NCBI Staff","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b"},"headline":"Updated bacterial and archaeal reference genomes collection now available!","datePublished":"2023-01-06T17:54:54+00:00","dateModified":"2023-01-06T19:56:53+00:00","mainEntityOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/"},"wordCount":181,"commentCount":1,"publisher":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage"},"thumbnailUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1","keywords":["Basic Local Alignment Search Tool (BLAST)","NCBI Taxonomy","Nucleotide BLAST (blastn)","Prokaryotic genome annotation","RefSeq"],"articleSection":["What's New"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/","name":"Updated bacterial and archaeal reference genomes collection now available! - NCBI Insights","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website"},"primaryImageOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage"},"thumbnailUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1","datePublished":"2023-01-06T17:54:54+00:00","dateModified":"2023-01-06T19:56:53+00:00","breadcrumb":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/01\/06\/bacterial-archaeal-reference-genomes\/#primaryimage","url":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1","contentUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1","width":1100,"height":575,"caption":"Colorful prokaryotic organisms in the background. 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