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The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO—a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations—evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)—mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

TheNLR‐receptorRPP7 mediates race‐specific immunity in Arabidopsis. Previous screens forenhanced downy mildew(edm) mutants identified the co‐chaperoneSGT1b (EDM1) and thePHD‐finger proteinEDM2 as critical regulators ofRPP7. Here, we describe a thirdedmmutant compromised inRPP7immunity,edm3.EDM3encodes a nuclear‐localized protein featuring anRNA‐recognition motif. LikeEDM2,EDM3 promotes histone H3 lysine 9 dimethylation (H3K9me2) atRPP7. Global profiling of H3K9me2 showedEDM3 to affect this silencing mark at a large set of loci. Importantly, bothEDM3 andEDM2 co‐associatein vivowith H3K9me2‐marked chromatin and transcripts at a critical proximal polyadenylation site ofRPP7, where they suppress proximal transcript polyadeylation/termination. Our results highlight the complexity of plantNLRgene regulation, and establish a functional and physical link between a histone mark andNLR‐transcript processing.

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.