{"id":12117,"date":"2023-09-18T14:17:35","date_gmt":"2023-09-18T18:17:35","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=12117"},"modified":"2023-09-18T14:17:35","modified_gmt":"2023-09-18T18:17:35","slug":"new-fungal-alignments-cgv","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/","title":{"rendered":"New Fungal Alignments Available in the Comparative Genome Viewer (CGV)"},"content":{"rendered":"

Recognizing Fungal Disease Awareness Week<\/span><\/i>\u00a0<\/span><\/h3>\n

Fungal pathogens are a growing threat to global public health. To promote awareness of this issue, the Centers for Disease Control and Prevention (CDC) has established September 18 -22 as <\/span>Fungal Disease Awareness Week<\/span><\/a>.\u00a0<\/span>\u00a0<\/span><\/p>\n

In honor of this week, we\u2019re highlighting whole genome alignments for fungal pathogens that are now available in the <\/span>Comparative Genome Viewer (CGV)<\/span><\/a> \u2013 NCBI\u2019s latest genome visualization tool.\u202f Alignment displays in CGV help you identify rearrangements and differences in genomic structure such as deletions, inversions, and translocations. These differences can be important for understanding genome plasticity, genetic diversity within species (<\/span>PMC8640552<\/span><\/a>) and the response to environmental stresses such as exposure to anti-fungal drugs (<\/span>PMC5555451<\/span><\/a>).\u202f\u202f\u202f<\/span>\u00a0<\/span><\/p>\n

CGV provides alignments for many species on the World Health Organization (WHO) <\/span>prioritized list of fungal pathogens<\/span><\/a> as well genome alignments of other fungi of medical, agricultural, or food production interest.<\/span>\u00a0<\/span><\/p>\n

You can explore cross-strain and cross-species genome alignments of several of these pathogens in <\/span>CGV<\/span><\/a>. Relevant species and some alignment partners are listed in the table below.<\/span>\u00a0<\/span><\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Species<\/strong><\/span><\/td>\nAssemblies in CGV<\/strong><\/span><\/td>\nCross-species<\/strong><\/span><\/td>\nWHO Priority\u202f\u00a0<\/strong><\/span><\/td>\n<\/tr>\n
Cryptococcus neoformans<\/em>\u202f\u00a0<\/span><\/td>\n5\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nCritical\u202f\u00a0<\/span><\/td>\n<\/tr>\n
[Candida] auris\u202f\u00a0<\/span><\/em><\/td>\n5\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nCritical\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Aspergillus fumigatus\u202f\u00a0<\/span><\/em><\/td>\n2\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nCritical\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Candida albicans\u202f\u00a0<\/span><\/em><\/td>\n3\u202f\u00a0<\/span><\/td>\nYes (C. dubliniensis)\u202f\u00a0<\/span><\/td>\nCritical\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Nakaseomyces glabratus\u202f\u00a0<\/span><\/em><\/td>\n4\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nHigh\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Fusarium oxysporum\u202f\u00a0<\/span><\/em><\/td>\n4\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nHigh\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Cryptococcus gattii\u202f\u00a0<\/span><\/em><\/td>\n2\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nMedium\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Pichia kudriavzevii\u202f\u00a0<\/span><\/em><\/td>\n2\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nMedium\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Talaromyces marneffei\u202f\u00a0<\/span><\/em><\/td>\n2\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nMedium\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Aspergillus flavus\u202f<\/em>\u00a0<\/span><\/td>\n3\u202f\u00a0<\/span><\/td>\nYes (A. oryzae)\u202f\u00a0<\/span><\/td>\nN\/A\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Aspergillus oryzae\u202f\u00a0<\/span><\/em><\/td>\n1\u202f\u00a0<\/span><\/td>\nYes (A. flavus)\u202f\u00a0<\/span><\/td>\nN\/A\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Aspergillus niger\u202f\u00a0<\/span><\/em><\/td>\n3\u202f\u00a0<\/span><\/td>\nNo\u202f\u00a0<\/span><\/td>\nN\/A\u202f\u00a0<\/span><\/td>\n<\/tr>\n
Candida dubliniensis<\/em>\u202f\u00a0<\/span><\/td>\n2\u202f\u00a0<\/span><\/td>\nYes (C. albicans)\u202f\u00a0<\/span><\/td>\nN\/A\u202f\u00a0<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Example<\/span><\/b>\u00a0<\/span><\/p>\n

\"ScreenshotFigure 1:<\/i><\/b> CGV alignment of a region of chromosome 5<\/a> for two <\/i>Talaromyces marneffei clinical isolate assemblies from Vietnam<\/i>. T. marneffei is a WHO medium priority pathogen that causes serious fungal infections. The two aligned assemblies are for strains associated with different disease severities. The alignment shows complex rearrangements in the region associated with the pathogenicity differences. See PMC6952663<\/a> for details.<\/i><\/span>\u00a0<\/span><\/p>\n

Stay up to date<\/h5>\n

CGV is a part of the\u202f<\/span>NIH Comparative Genomics Resource (CGR)<\/span><\/a>. CGR facilitates reliable comparative genomics analyses\u202ffor all eukaryotic organisms through an NCBI Toolkit and community collaboration.\u202f\u202f\u202f\u202f<\/span>\u00a0<\/span><\/p>\n

Follow us on social\u202f<\/span>@NCBI<\/span><\/a>\u202fand\u202f<\/span>join our mailing list<\/span><\/a>\u202fto keep up to date with CGV and other CGR news.\u202f\u202f\u202f\u202f\u202f<\/span>\u00a0<\/span><\/p>\n

Questions?<\/h5>\n

If you have questions or would like to provide feedback, please <\/span>write to our help desk<\/span><\/a>.\u00a0\u00a0<\/span>\u00a0<\/span><\/p>\n

\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Recognizing Fungal Disease Awareness Week\u00a0 Fungal pathogens are a growing threat to global public health. To promote awareness of this issue, the Centers for Disease Control and Prevention (CDC) has established September 18 -22 as Fungal Disease Awareness Week.\u00a0\u00a0 In honor of this week, we\u2019re highlighting whole genome alignments for fungal pathogens that are now … Continue reading New Fungal Alignments Available in the Comparative Genome Viewer (CGV)<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":12119,"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":"New Fungal Alignments Available in the Comparative Genome Viewer (CGV)","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":[693060769,693060768,354510227],"table_tags":[],"class_list":["post-12117","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-comparative-genome-viewer-cgv","tag-comparative-genomics-resource-cgr","tag-fungal-research"],"jetpack_publicize_connections":[],"yoast_head":"\nNew Fungal Alignments Available in the Comparative Genome Viewer (CGV) - 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\/09\/18\/new-fungal-alignments-cgv\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"New Fungal Alignments Available in the Comparative Genome Viewer (CGV) - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Recognizing Fungal Disease Awareness Week\u00a0 Fungal pathogens are a growing threat to global public health. 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To promote awareness of this issue, the Centers for Disease Control and Prevention (CDC) has established September 18 -22 as Fungal Disease Awareness Week.\u00a0\u00a0 In honor of this week, we\u2019re highlighting whole genome alignments for fungal pathogens that are now … Continue reading New Fungal Alignments Available in the Comparative Genome Viewer (CGV) →","og_url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/","og_site_name":"NCBI Insights","article_publisher":"https:\/\/www.facebook.com\/ncbi.nlm","article_published_time":"2023-09-18T18:17:35+00:00","og_image":[{"width":1100,"height":575,"url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/CGV_Fungal_Alignments-1-e1695057681679.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":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#article","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/"},"author":{"name":"NCBI Staff","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b"},"headline":"New Fungal Alignments Available in the Comparative Genome Viewer (CGV)","datePublished":"2023-09-18T18:17:35+00:00","mainEntityOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/"},"wordCount":383,"commentCount":0,"publisher":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#primaryimage"},"thumbnailUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/CGV_Fungal_Alignments-1-e1695057681679.png?fit=1100%2C575&ssl=1","keywords":["Comparative Genome Viewer (CGV)","Comparative Genomics Resource (CGR)","Fungal research"],"articleSection":["What's New"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/","name":"New Fungal Alignments Available in the Comparative Genome Viewer (CGV) - NCBI Insights","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website"},"primaryImageOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#primaryimage"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#primaryimage"},"thumbnailUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/CGV_Fungal_Alignments-1-e1695057681679.png?fit=1100%2C575&ssl=1","datePublished":"2023-09-18T18:17:35+00:00","breadcrumb":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/18\/new-fungal-alignments-cgv\/#primaryimage","url":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/CGV_Fungal_Alignments-1-e1695057681679.png?fit=1100%2C575&ssl=1","contentUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/CGV_Fungal_Alignments-1-e1695057681679.png?fit=1100%2C575&ssl=1","width":1100,"height":575,"caption":"Green and blue lines representing genome alignments in the CGV. Text says: Comparative Genome Viewer (CGV) New Fungal Alignments Available. 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