{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:19:25Z","timestamp":1758845965250,"version":"3.44.0"},"reference-count":49,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T00:00:00Z","timestamp":1758758400000},"content-version":"vor","delay-in-days":267,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["2022.00397.CEECIND\/CP1728\/CT0006","2023.07615.CEECIND\/CP2848\/CT0007","CEECINST\/00133\/2018\/CP1510\/CT0004"],"award-info":[{"award-number":["2022.00397.CEECIND\/CP1728\/CT0006","2023.07615.CEECIND\/CP2848\/CT0007","CEECINST\/00133\/2018\/CP1510\/CT0004"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Molecular databases are essential resources for both experimental and computational biologists. The rapid increase in high-quality genome assemblies has led to a surge in publications describing secondary gene loss events associated with lineage-specific adaptations across diverse vertebrate groups. This growing volume of information underscores the urgent need for organized, searchable, and curated resources that facilitate data discovery, allow detection of broad evolutionary patterns, and support downstream analyses. Currently, no existing database compiles manually curated and validated information on published secondary gene loss events. Here, we introduce the Gene Loss Database (Gene Loss DB), a platform designed to centralize and present these data in an easy-to-search and user-friendly format (https:\/\/geneloss.org\/). Gene Loss DB compiles gene loss events alongside supporting evidence, including the inferred mechanism of gene loss (exon deletion, gene deletion, loss of function mutation), the type of data used to support inactivation (genomic, transcriptomic, single\/multiple individual sequence reads, synteny maps) and, when available, whether the event is shared across all lineages within a taxon. Each entry also includes a short excerpt from the original publication to provide context. This information is structured in the database to be searchable by species, gene, taxa, or by gene ontology terms linked to the gene in question. The initial release of Gene Loss DB focuses on cetaceans, a lineage with numerous gene loss events linked to aquatic adaptations. This first collection comprises 1872 gene loss events identified across 57 cetacean species. In addition, the database includes 1321 gene loss events from other taxa, which were also reported in the same studies and collected simultaneously.<\/jats:p>","DOI":"10.1093\/database\/baaf065","type":"journal-article","created":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:26:49Z","timestamp":1758810409000},"source":"Crossref","is-referenced-by-count":0,"title":["Gene Loss DB: a curated database for gene loss in mammals\u2014the cetacean collection"],"prefix":"10.1093","volume":"2025","author":[{"given":"Gon\u00e7alo Espregueira","family":"Themudo","sequence":"first","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]}]},{"given":"Raquel","family":"Ruivo","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]}]},{"given":"Raul","family":"Valente","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]}]},{"given":"N\u00e1dia","family":"Artilheiro","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]}]},{"given":"Diogo","family":"Oliveira","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]},{"name":"University of Porto Department of Biology, Faculty of Science, , Rua Campo Alegre s\/n, 4169-007 Porto ,","place":["Portugal"]}]},{"given":"In\u00eas","family":"Amorim","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]},{"name":"ICBAS, Abel Salazar Institute of Biomedical Sciences, University do Porto , Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto ,","place":["Portugal"]}]},{"given":"Bernardo","family":"Pinto","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]}]},{"given":"Lu\u00eds Filipe C","family":"Castro","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]},{"name":"University of Porto Department of Biology, Faculty of Science, , Rua Campo Alegre s\/n, 4169-007 Porto ,","place":["Portugal"]}]},{"given":"Sergio","family":"Fernandes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8597-4730","authenticated-orcid":false,"given":"M\u00f3nica","family":"Lopes-Marques","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos, S\/N 4450-208 Matosinhos ,","place":["Portugal"]},{"name":"University of Porto Department of Biology, Faculty of Science, , Rua Campo Alegre s\/n, 4169-007 Porto ,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2025,9,24]]},"reference":[{"key":"2025092510264156400_bib1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.semcdb.2012.12.008","article-title":"Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates","volume":"24","author":"Ca\u00f1estro","year":"2013","journal-title":"Semin Cell Dev Biol"},{"key":"2025092510264156400_bib2","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nrg.2016.39","article-title":"Evolution by gene loss","volume":"17","author":"Albalat","year":"2016","journal-title":"Nat Rev Genet"},{"key":"2025092510264156400_bib3","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1086\/302219","article-title":"When less is more: gene loss as an engine of evolutionary change","volume":"64","author":"Olson","year":"1999","journal-title":"Am Hum Genet"},{"key":"2025092510264156400_bib4","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1038\/s41467-018-03667-1","article-title":"A genomics approach reveals insights into the importance of gene losses for mammalian adaptations","volume":"9","author":"Sharma","year":"2018","journal-title":"Nat Commun"},{"key":"2025092510264156400_bib5","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1126\/science.1058543","article-title":"Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis","volume":"292","author":"Ochman","year":"2001","journal-title":"Science"},{"key":"2025092510264156400_bib6","doi-asserted-by":"publisher","first-page":"2204","DOI":"10.1111\/nph.19242","article-title":"Genome evolution in plants and the origins of innovation","volume":"240","author":"Clark","year":"2023","journal-title":"New Phytol"},{"key":"2025092510264156400_bib7","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41559-020-1129-2","article-title":"Widespread patterns of gene loss in the evolution of the animal kingdom","volume":"4","author":"Guijarro-Clarke","year":"2020","journal-title":"Nat Ecol Evol"},{"key":"2025092510264156400_bib8","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/j.mib.2012.07.008","article-title":"Bacterial gene loss as a mechanism for gain of antimicrobial resistance","volume":"15","author":"T\u00f6r\u00f6k","year":"2012","journal-title":"Curr Opin Microbiol"},{"key":"2025092510264156400_bib9","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1093\/molbev\/msn012","article-title":"Identification of novel mammalian caspases reveals an important role of gene loss in shaping the human caspase repertoire","volume":"25","author":"Eckhart","year":"2008","journal-title":"Mol Biol Evol"},{"key":"2025092510264156400_bib10","first-page":"20132669","article-title":"Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history","volume":"281","author":"Castro","year":"2014","journal-title":"Proc Biol Sci"},{"key":"2025092510264156400_bib11","volume-title":"The NCBI Handbook","author":"Thibaud-Nissen\u00a0F","year":"2013","edition":"2nd edn"},{"key":"2025092510264156400_bib12","doi-asserted-by":"publisher","first-page":"eabm6494","DOI":"10.1126\/sciadv.abm6494","article-title":"Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding","volume":"8","author":"Blumer","year":"2022","journal-title":"Sci Adv"},{"key":"2025092510264156400_bib13","doi-asserted-by":"publisher","first-page":"1270","DOI":"10.1093\/molbev\/msz068","article-title":"Complete inactivation of sebum-producing genes parallels the loss of sebaceous glands in cetacea","volume":"36","author":"Lopes-Marques","year":"2019","journal-title":"Mol Biol Evol"},{"key":"2025092510264156400_bib14","doi-asserted-by":"publisher","first-page":"121","DOI":"10.3390\/genes10020121","article-title":"The singularity of cetacea behavior parallels the complete inactivation of melatonin gene modules","volume":"10","author":"Lopes-Marques","year":"2019","journal-title":"Genes"},{"key":"2025092510264156400_bib15","doi-asserted-by":"publisher","first-page":"121458","DOI":"10.1007\/s00239-023-10118-z","article-title":"Decay of skin-specific gene modules in pangolins","volume":"91","author":"Pinto","year":"2023","journal-title":"J Mol Evol"},{"key":"2025092510264156400_bib16","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s00251-018-1071-5","article-title":"Cetacea are natural knockouts for IL20","volume":"70","author":"Lopes-Marques","year":"2018","journal-title":"Immunogenetics"},{"key":"2025092510264156400_bib17","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/j.ympev.2017.08.014","article-title":"Unusual loss of chymosin in mammalian lineages parallels neo-natal immune transfer strategies","volume":"116","author":"Lopes-Marques","year":"2017","journal-title":"Mol Phylogenet Evol"},{"key":"2025092510264156400_bib18","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1186\/1471-2164-15-869","article-title":"Increased rate of hair keratin gene loss in the cetacean lineage","volume":"15","author":"Nery","year":"2014","journal-title":"BMC Genomics [Electronic Resource]"},{"key":"2025092510264156400_bib19","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1186\/s12862-014-0218-8","article-title":"The loss of taste genes in cetaceans","volume":"14","author":"Zhu","year":"2014","journal-title":"BMC Evol Biol"},{"key":"2025092510264156400_bib20","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1007\/s11427-022-2195-x","article-title":"Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla","volume":"66","author":"Lang","year":"2023","journal-title":"Sci China Life Sci"},{"key":"2025092510264156400_bib21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10709-021-00113-x","article-title":"Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms","volume":"149","author":"van\u00a0Asch","year":"2021","journal-title":"Genetica"},{"key":"2025092510264156400_bib22","first-page":"993","article-title":"Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales","volume":"278","author":"Meredith","year":"2011","journal-title":"Proc Biol Sci"},{"key":"2025092510264156400_bib23","doi-asserted-by":"publisher","first-page":"e1000634","DOI":"10.1371\/journal.pgen.1000634","article-title":"Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals","volume":"5","author":"Meredith","year":"2009","journal-title":"PLoS Genet"},{"key":"2025092510264156400_bib24","doi-asserted-by":"publisher","first-page":"W321","DOI":"10.1093\/nar\/gkaa408","article-title":"PseudoChecker: an integrated online platform for gene inactivation inference","volume":"48","author":"Alves","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025092510264156400_bib25","doi-asserted-by":"publisher","first-page":"eabn3107","DOI":"10.1126\/science.abn3107","article-title":"Integrating gene annotation with orthology inference at scale","volume":"380","author":"Kirilenko","year":"2023","journal-title":"Science"},{"key":"2025092510264156400_bib26","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1093\/icb\/icy004","article-title":"Regressed but not gone: patterns of vision gene loss and retention in subterranean mammals","volume":"58","author":"Emerling","year":"2018","journal-title":"Integr Comp Biol"},{"key":"2025092510264156400_bib27","doi-asserted-by":"publisher","first-page":"eaaw6671","DOI":"10.1126\/sciadv.aaw6671","article-title":"Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations","volume":"5","author":"Huelsmann","year":"2019","journal-title":"Sci Adv"},{"key":"2025092510264156400_bib28","doi-asserted-by":"publisher","first-page":"e1003432","DOI":"10.1371\/journal.pgen.1003432","article-title":"Rod monochromacy and the coevolution of cetacean retinal opsins","volume":"9","author":"Meredith","year":"2013","journal-title":"PLoS Genet"},{"key":"2025092510264156400_bib29","doi-asserted-by":"publisher","first-page":"40233","DOI":"10.1038\/srep40233","article-title":"Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans","volume":"7","author":"Nam","year":"2017","journal-title":"Sci Rep"},{"key":"2025092510264156400_bib30","doi-asserted-by":"publisher","first-page":"evab201","DOI":"10.1093\/gbe\/evab201","article-title":"Parallel independent losses of G-type lysozyme genes in hairless aquatic mammals","volume":"13","author":"Zhang","year":"2021","journal-title":"Genome Biol Evolut"},{"key":"2025092510264156400_bib31","doi-asserted-by":"publisher","first-page":"12334","DOI":"10.1038\/s41598-021-91863-3","article-title":"Gene duplications and gene loss in the epidermal differentiation complex during the evolutionary land-to-water transition of cetaceans","volume":"11","author":"Holthaus","year":"2021","journal-title":"Sci Rep"},{"key":"2025092510264156400_bib32","doi-asserted-by":"publisher","first-page":"17446","DOI":"10.1038\/s41598-017-17782-4","article-title":"Epidermal cornification is preceded by the expression of a keratinocyte-specific set of pyroptosis-related genes","volume":"7","author":"Lachner","year":"2017","journal-title":"Sci Rep"},{"key":"2025092510264156400_bib33","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1007\/s00251-019-01114-z","article-title":"Convergent inactivation of the skin-specific C-C motif chemokine ligand 27 in mammalian evolution","volume":"71","author":"Lopes-Marques","year":"2019","journal-title":"Immunogenetics"},{"key":"2025092510264156400_bib34","doi-asserted-by":"publisher","first-page":"107463","DOI":"10.1016\/j.ympev.2022.107463","article-title":"Molecular evolutionary analyses of tooth genes support sequential loss of enamel and teeth in baleen whales (Mysticeti)","volume":"171","author":"Randall","year":"2022","journal-title":"Mol Phylogenet Evol"},{"key":"2025092510264156400_bib35","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1080\/10635150701884632","article-title":"Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in Mysticete whales","volume":"57","author":"Dem\u00e9r\u00e9","year":"2008","journal-title":"Syst Biol"},{"key":"2025092510264156400_bib36","doi-asserted-by":"publisher","first-page":"2069","DOI":"10.1093\/molbev\/msaa070","article-title":"Positive selection and inactivation in the vision and hearing genes of cetaceans","volume":"37","author":"McGowen","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2025092510264156400_bib37","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1098\/rspb.2002.2278","article-title":"Genetic evidence for the ancestral loss of short-wavelength-sensitive cone pigments in mysticete and odontocete cetaceans","volume":"270","author":"Levenson","year":"2003","journal-title":"Proc Biol Sci"},{"key":"2025092510264156400_bib38","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1002\/pro.4218","article-title":"PANTHER: making genome-scale phylogenetics accessible to all","volume":"31","author":"Thomas","year":"2022","journal-title":"Protein Sci"},{"key":"2025092510264156400_bib39","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/978-1-60761-175-2_7","article-title":"PANTHER pathway: an ontology-based pathway database coupled with data analysis tools","volume":"563","author":"Mi","year":"2009","journal-title":"Methods Mol Biol"},{"key":"2025092510264156400_bib40","doi-asserted-by":"publisher","first-page":"D20","DOI":"10.1093\/nar\/gkae979","article-title":"Database resources of the National Center for Biotechnology Information in 2025","volume":"53","author":"Sayers","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2025092510264156400_bib41","doi-asserted-by":"publisher","first-page":"W540","DOI":"10.1093\/nar\/gkae235","article-title":"PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge","volume":"52","author":"Wei","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025092510264156400_bib42","doi-asserted-by":"publisher","first-page":"2020","DOI":"10.3389\/fmars.2020.592375","article-title":"Losing genes: the evolutionary remodeling of cetacea skin","volume":"7","author":"Espregueira\u00a0Themudo","year":"2020","journal-title":"Front Mar Sci"},{"key":"2025092510264156400_bib43","doi-asserted-by":"publisher","first-page":"11565","DOI":"10.1038\/s41598-020-68106-y","article-title":"GBA3: a polymorphic pseudogene in humans that experienced repeated gene loss during mammalian evolution","volume":"10","author":"Lopes-Marques","year":"2020","journal-title":"Sci Rep"},{"key":"2025092510264156400_bib44","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1007\/s00439-024-02715-9","article-title":"Polymorphic pseudogenes in the human genome\u2014a comprehensive assessment","volume":"143","author":"Lopes-Marques","year":"2024","journal-title":"Hum Genet"},{"key":"2025092510264156400_bib45","doi-asserted-by":"publisher","first-page":"9278","DOI":"10.1038\/s41598-024-60099-2","article-title":"Comparative genomics of sirenians reveals evolution of filaggrin and caspase-14 upon adaptation of the epidermis to aquatic life","volume":"14","author":"Steinbinder","year":"2024","journal-title":"Sci Rep"},{"key":"2025092510264156400_bib46","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1016\/j.ygeno.2020.11.002","article-title":"Convergent Cortistatin losses parallel modifications in circadian rhythmicity and energy homeostasis in Cetacea and other mammalian lineages","volume":"113","author":"Valente","year":"2021","journal-title":"Genomics"},{"key":"2025092510264156400_bib47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.margen.2018.08.004","article-title":"On the revolution of cetacean evolution","volume":"41","author":"Mancia","year":"2018","journal-title":"Mar Geonomics"},{"key":"2025092510264156400_bib48","doi-asserted-by":"publisher","first-page":"2233","DOI":"10.1016\/j.cub.2022.04.060","article-title":"The tempo of cetacean cranial evolution","volume":"32","author":"Coombs","year":"2022","journal-title":"Curr Biol"},{"key":"2025092510264156400_bib49","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaf065\/64394807\/baaf065.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaf065\/64394807\/baaf065.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:26:51Z","timestamp":1758810411000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaf065\/8263858"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":49,"URL":"https:\/\/doi.org\/10.1093\/database\/baaf065","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"baaf065"}}