{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T14:25:54Z","timestamp":1780064754079,"version":"3.54.0"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T00:00:00Z","timestamp":1750809600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In silico gene annotation, the process of identifying the genes present in a genome, remains a challenging task. As genome assemblies rapidly increase, the corresponding gene models and repertoires often fall short in quality. Despite advances in annotation methods, a lack of community standards means that most published gene annotations result from ad hoc pipelines. As a result, only a few species have nearly complete and accurate gene models. This annotation quality is thought to affect downstream analyses, including orthology inference, often the first step of comparative genomics studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We show that different annotation methods yield markedly distinct orthology inferences. We compared orthology assignments of gene models obtained by four prominent protein-coding gene model sources: the NCBI Eukaryotic Genome Annotation Pipeline, the Ensembl Gene Annotation System, the UniProt Reference Proteomes, and Augustus 3.4 (an ab initio pipeline). We observe significant discrepancies between sources, namely in the proportion of orthologous genes per genome, the completeness of Hierarchical Orthologous Groups, and the accuracy and recall of the predicted orthologs on a standard orthology benchmark.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf365","type":"journal-article","created":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T11:25:07Z","timestamp":1750850707000},"source":"Crossref","is-referenced-by-count":12,"title":["Annotation matters: the effect of structural gene annotation on orthology inference"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-5042-2323","authenticated-orcid":false,"given":"Silvia","family":"Prieto-Ba\u00f1os","sequence":"first","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne, 1015,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Lausanne, 1015,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8604-2943","authenticated-orcid":false,"given":"Yannis","family":"Nevers","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne, 1015,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Lausanne, 1015,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian","family":"Altenhoff","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics , Lausanne, 1015,","place":["Switzerland"]},{"name":"Computer Science, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4074-4261","authenticated-orcid":false,"given":"Alex","family":"Warwick Vesztrocy","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne, 1015,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Lausanne, 1015,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2170-853X","authenticated-orcid":false,"given":"Christophe","family":"Dessimoz","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne, 1015,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Lausanne, 1015,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha M","family":"Glover","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne, 1015,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Lausanne, 1015,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,25]]},"reference":[{"key":"2025071516412289200_btaf365-B1","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1186\/s12864-024-10521-w","article-title":"Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies","volume":"25","author":"Abbas","year":"2024","journal-title":"BMC Genomics"},{"key":"2025071516412289200_btaf365-B2","doi-asserted-by":"crossref","first-page":"baw093","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","volume":"2016","author":"Aken","year":"2016","journal-title":"Database"},{"key":"2025071516412289200_btaf365-B3","doi-asserted-by":"crossref","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":"2025071516412289200_btaf365-B4","doi-asserted-by":"crossref","first-page":"D373","DOI":"10.1093\/nar\/gkaa1007","article-title":"OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more","volume":"49","author":"Altenhoff","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B5","article-title":"OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA ecosystem","volume":"52","author":"Altenhoff","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B6","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1101\/gr.243212.118","article-title":"OMA standalone: orthology inference among public and custom genomes and transcriptomes","volume":"29","author":"Altenhoff","year":"2019","journal-title":"Genome Res"},{"key":"2025071516412289200_btaf365-B7","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nmeth.3830","article-title":"Standardized benchmarking in the quest for orthologs","volume":"13","author":"Altenhoff","year":"2016","journal-title":"Nat Methods"},{"key":"2025071516412289200_btaf365-B8","doi-asserted-by":"crossref","first-page":"30700","DOI":"10.1038\/srep30700","article-title":"Putative extremely high rate of proteome innovation in lancelets might be explained by high rate of gene prediction errors","volume":"6","author":"B\u00e1nyai","year":"2016","journal-title":"Sci Rep"},{"key":"2025071516412289200_btaf365-B9","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"GeneWise and genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2025071516412289200_btaf365-B10","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2115636118","article-title":"Why sequence all eukaryotes?","volume":"119","author":"Blaxter","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025071516412289200_btaf365-B11","doi-asserted-by":"publisher","author":"Brown","year":"2024","DOI":"10.37044\/osf.io\/fy49g,"},{"key":"2025071516412289200_btaf365-B12","doi-asserted-by":"crossref","first-page":"lqaa108","DOI":"10.1093\/nargab\/lqaa108","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database","volume":"3","author":"Br\u016fna","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2025071516412289200_btaf365-B13","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1186\/s12859-023-05449-z","article-title":"GALBA: genome annotation with miniprot and AUGUSTUS","volume":"24","author":"Br\u016fna","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2025071516412289200_btaf365-B14","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1101\/gr.278373.123","article-title":"GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes","volume":"34","author":"Br\u016fna","year":"2024","journal-title":"Genome Res"},{"key":"2025071516412289200_btaf365-B15","first-page":"2906","article-title":"From de novo to \u201cde nono\u201d: the majority of novel protein-coding genes identified with phylostratigraphy are old genes or recent duplicates","volume":"10","author":"Casola","year":"2018","journal-title":"Genome Biol Evol"},{"key":"2025071516412289200_btaf365-B16","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022","volume":"50","author":"Cunningham","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B17","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2025071516412289200_btaf365-B18","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/s41586-020-2873-9","article-title":"Dense sampling of bird diversity increases power of comparative genomics","volume":"587","author":"Feng","year":"2020","journal-title":"Nature"},{"key":"2025071516412289200_btaf365-B19","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nrg3456","article-title":"Functional and evolutionary implications of gene orthology","volume":"14","author":"Gabald\u00f3n","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2025071516412289200_btaf365-B20","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1101\/gr.278090.123","article-title":"BRAKER3: fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA","volume":"34","author":"Gabriel","year":"2024","journal-title":"Genome Res"},{"key":"2025071516412289200_btaf365-B21","doi-asserted-by":"crossref","first-page":"btae685","DOI":"10.1093\/bioinformatics\/btae685","article-title":"Tiberius: end-to-end deep learning with an HMM for gene prediction","volume":"40","author":"Gabriel","year":"2024","journal-title":"Bioinformatics"},{"key":"2025071516412289200_btaf365-B22","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/molbev\/msz150","article-title":"Advances and applications in the quest for orthologs","volume":"36","author":"Glover","year":"2019","journal-title":"Mol Biol Evol"},{"key":"2025071516412289200_btaf365-B23","doi-asserted-by":"crossref","first-page":"D243","DOI":"10.1093\/nar\/gkae1038","article-title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","volume":"53","author":"Goldfarb","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B24","doi-asserted-by":"crossref","first-page":"100375","DOI":"10.1016\/j.xgen.2023.100375","article-title":"Genome annotation: from human genetics to biodiversity genomics","volume":"3","author":"Guig\u00f3","year":"2023","journal-title":"Cell Genom"},{"key":"2025071516412289200_btaf365-B25","doi-asserted-by":"crossref","first-page":"msab310","DOI":"10.1093\/molbev\/msab310","article-title":"Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of Salmonid evolution","volume":"39","author":"Gundappa","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2025071516412289200_btaf365-B26","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1002\/cpbi.57","article-title":"Predicting genes in single genomes with AUGUSTUS","volume":"65","author":"Hoff","year":"2019","journal-title":"Curr Protoc Bioinform"},{"key":"2025071516412289200_btaf365-B27","doi-asserted-by":"publisher","author":"Holst","DOI":"10.1101\/2023.02.06.527280,"},{"key":"2025071516412289200_btaf365-B28","doi-asserted-by":"crossref","first-page":"14918","DOI":"10.1073\/pnas.1507669112","article-title":"Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling","volume":"112","author":"Inoue","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025071516412289200_btaf365-B29","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/978-1-4939-9173-0_9","article-title":"GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data","volume":"1962","author":"Keilwagen","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2025071516412289200_btaf365-B30","doi-asserted-by":"crossref","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":"2025071516412289200_btaf365-B31","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1146\/annurev-animal-090414-014900","article-title":"The Genome 10K Project: a way forward","volume":"3","author":"Koepfli","year":"2015","journal-title":"Annu Rev Anim Biosci"},{"key":"2025071516412289200_btaf365-B6774567","doi-asserted-by":"publisher","first-page":"1178926","DOI":"10.3389\/fbinf.2023.1178926","article-title":"Real or fake? measuring the impact of protein annotation errors on estimates of domain gain and loss events","volume":"3","author":"Kress","year":"2023","journal-title":"Front Bioinform"},{"key":"2025071516412289200_btaf365-B32","doi-asserted-by":"crossref","first-page":"D807","DOI":"10.1093\/nar\/gky1053","article-title":"OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs","volume":"47","author":"Kriventseva","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B33","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac174","article-title":"TimeTree 5: an expanded resource for species divergence times","volume":"39","author":"Kumar","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2025071516412289200_btaf365-B34","doi-asserted-by":"crossref","DOI":"10.1093\/gbe\/evae224","article-title":"Quest for orthologs in the era of biodiversity genomics","volume":"16","author":"Langschied","year":"2024","journal-title":"Genome Biol Evol"},{"key":"2025071516412289200_btaf365-B35","doi-asserted-by":"crossref","first-page":"4325","DOI":"10.1073\/pnas.1720115115","article-title":"Earth BioGenome project: sequencing life for the future of life","volume":"115","author":"Lewin","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025071516412289200_btaf365-B36","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/nature17164","article-title":"The Atlantic salmon genome provides insights into rediploidization","volume":"533","author":"Lien","year":"2016","journal-title":"Nature"},{"key":"2025071516412289200_btaf365-B37","doi-asserted-by":"crossref","first-page":"3033","DOI":"10.1093\/molbev\/msab098","article-title":"Ten years of collaborative progress in the Quest for orthologs","volume":"38","author":"Linard","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025071516412289200_btaf365-B38","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025071516412289200_btaf365-B39","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/s13059-023-02973-2","article-title":"Protein length distribution is remarkably uniform across the tree of life","volume":"24","author":"Nevers","year":"2023","journal-title":"Genome Biol"},{"key":"2025071516412289200_btaf365-B40","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41587-024-02147-w","article-title":"Quality assessment of gene repertoire annotations with OMArk","volume":"43","author":"Nevers","year":"2025","journal-title":"Nat Biotechnol"},{"key":"2025071516412289200_btaf365-B41","doi-asserted-by":"crossref","first-page":"W623","DOI":"10.1093\/nar\/gkac330","article-title":"The Quest for orthologs orthology benchmark service in 2022","volume":"50","author":"Nevers","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B42","doi-asserted-by":"crossref","first-page":"304","DOI":"10.12688\/f1000research.23297.1","article-title":"GFF utilities: GffRead and GffCompare","volume":"9","author":"Pertea","year":"2020","journal-title":"F1000Res"},{"key":"2025071516412289200_btaf365-B43","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2025071516412289200_btaf365-B44","doi-asserted-by":"crossref","first-page":"evae128","DOI":"10.1093\/gbe\/evae128","article-title":"Molecular dating of the teleost whole genome duplication (3R) is compatible with the expectations of delayed rediploidization","volume":"16","author":"Qi","year":"2024","journal-title":"Genome Biol Evol"},{"key":"2025071516412289200_btaf365-B45","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"Rhie","year":"2021","journal-title":"Nature"},{"key":"2025071516412289200_btaf365-B46","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/s13059-019-1715-2","article-title":"Next-generation genome annotation: we still struggle to get it right","volume":"20","author":"Salzberg","year":"2019","journal-title":"Genome Biol"},{"key":"2025071516412289200_btaf365-B47","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1186\/s12864-020-6707-9","article-title":"A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms","volume":"21","author":"Scalzitti","year":"2020","journal-title":"BMC Genomics"},{"key":"2025071516412289200_btaf365-B48","doi-asserted-by":"crossref","first-page":"4370","DOI":"10.1038\/ncomms5370","article-title":"Primate evolution of the recombination regulator PRDM9","volume":"5","author":"Schwartz","year":"2014","journal-title":"Nat Commun"},{"key":"2025071516412289200_btaf365-B49","doi-asserted-by":"crossref","first-page":"lqae189","DOI":"10.1093\/nargab\/lqae189","article-title":"PSAURON: a tool for assessing protein annotation across a broad range of species","volume":"7","author":"Sommer","year":"2025","journal-title":"NAR Genom Bioinform"},{"key":"2025071516412289200_btaf365-B50","doi-asserted-by":"crossref","first-page":"ii215","DOI":"10.1093\/bioinformatics\/btg1080","article-title":"Gene prediction with a hidden Markov model and a new intron submodel","volume":"19 Suppl 2","author":"Stanke","year":"2003","journal-title":"Bioinformatics"},{"key":"2025071516412289200_btaf365-B51","doi-asserted-by":"crossref","first-page":"184","DOI":"10.2527\/jas2016.94supplement4184x","article-title":"P8008 the NCBI eukaryotic genome annotation pipeline","volume":"94","author":"Thibaud-Nissen","year":"2016","journal-title":"J Anim Sci"},{"key":"2025071516412289200_btaf365-B52","doi-asserted-by":"crossref","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":"2025071516412289200_btaf365-B53","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1186\/1756-0500-5-85","article-title":"Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes","volume":"5","author":"Tiessen","year":"2012","journal-title":"BMC Res Notes"},{"key":"2025071516412289200_btaf365-B54","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1093\/molbev\/msn281","article-title":"Origin of primate orphan genes: a comparative genomics approach","volume":"26","author":"Toll-Riera","year":"2009","journal-title":"Mol Biol Evol"},{"key":"2025071516412289200_btaf365-B55","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1002\/bies.201100062","article-title":"Orthology prediction methods: a quality assessment using curated protein families","volume":"33","author":"Trachana","year":"2011","journal-title":"Bioessays"},{"key":"2025071516412289200_btaf365-B56","doi-asserted-by":"crossref","first-page":"i75","DOI":"10.1093\/bioinformatics\/btx229","article-title":"Orthologous matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference","volume":"33","author":"Train","year":"2017","journal-title":"Bioinformatics"},{"key":"2025071516412289200_btaf365-B57","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the Universal Protein Knowledgebase in 2023","volume":"51","author":"UniProt Consortium","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071516412289200_btaf365-B58","doi-asserted-by":"crossref","first-page":"evae151","DOI":"10.1093\/gbe\/evae151","article-title":"Ancestral sequence reconstruction as a tool to detect and study de novo gene emergence","volume":"16","author":"Vakirlis","year":"2024","journal-title":"Genome Biol Evol"},{"key":"2025071516412289200_btaf365-B59","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1111\/jeb.14181","article-title":"Understanding the evolution of immune genes in jawed vertebrates","volume":"36","author":"Vinkler","year":"2023","journal-title":"J Evol Biol"},{"key":"2025071516412289200_btaf365-B60","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat Methods"},{"key":"2025071516412289200_btaf365-B61","doi-asserted-by":"crossref","first-page":"e11533","DOI":"10.1002\/aps3.11533","article-title":"Welcome to the big leaves: best practices for improving genome annotation in non-model plant genomes","volume":"11","author":"Vuruputoor","year":"2023","journal-title":"Appl Plant Sci"},{"key":"2025071516412289200_btaf365-B62","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1016\/j.cub.2022.04.085","article-title":"Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes","volume":"32","author":"Weisman","year":"2022","journal-title":"Curr Biol"},{"key":"2025071516412289200_btaf365-B63","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nrg3174","article-title":"A beginner\u2019s guide to eukaryotic genome annotation","volume":"13","author":"Yandell","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2025071516412289200_btaf365-B64","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41559-019-0822-5","article-title":"Rapid evolution of protein diversity by de novo origination in Oryza","volume":"3","author":"Zhang","year":"2019","journal-title":"Nat Ecol Evol"},{"key":"2025071516412289200_btaf365-B65","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1146\/annurev-genet-111523-102413","article-title":"De novo genes","volume":"58","author":"Zhao","year":"2024","journal-title":"Annu Rev Genet"},{"key":"2025071516412289200_btaf365-B66","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1093\/gbe\/evaa127","article-title":"Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence","volume":"12","author":"Zile","year":"2020","journal-title":"Genome Biol Evol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf365\/63580423\/btaf365.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/7\/btaf365\/63580423\/btaf365.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/7\/btaf365\/63580423\/btaf365.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T20:41:33Z","timestamp":1752612093000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf365\/8173798"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,6,25]]},"references-count":67,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2025,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf365","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,6,25]]},"article-number":"btaf365"}}