ArticleNucleic acids research2022
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
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Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 245 papers, 5 of them syntheses that pooled it.
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245citing papers in PubMed, 5 pooled it
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Who cites it
245 citing papers in PubMed, 5 syntheses or guidelines pooled it.
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- Serum liver enzymes and risk of stroke: Systematic review with meta-analyses and Mendelian randomization studies.European journal of neurology · 2024Pooled it
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- Distinct associations of ScGDD1/BC12 transcript abundance and sequence variation with grain size and shape in rye.Journal of applied genetics · 2026Article
- A grass-specific structural myosin VIII regulates protoxylem development and hydraulic conductance in sorghum.Plant physiology · 2026Article
- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
- Evolution of the α-Glucosidase Gene Family in Apoidea.Ecology and evolution · 2026Article
- Evolutionary diversification of invertase paralogs couples carbon metabolism and sexual reproduction in fission yeasts.Molecular biology and evolution · 2026Article
- Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes.Genes & development · 2026Article
- A conserved small RNA-generating gene cluster undergoes sequence diversification and contributes to plant immunity.Nature communications · 2026Article
- Genome-Wide Characterization and Salt-Responsive Expression Divergence of Chromosome Group 2 and Group 6Plants (Basel, Switzerland) · 2026Article
- Odorant receptor coexpression and multi-expression in the dengue mosquito.Nature communications · 2026Article
- Range-Wide Genetic Population Structure and Environmental Adaptation in the Eastern Oyster (Crassostrea virginica) Provides Insight for Aquaculture.Molecular ecology · 2026Article
- Genome-Wide Identification ofPlants (Basel, Switzerland) · 2026Article
- Investigating GERMs: how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum.The New phytologist · 2026Article
- Mammalian-evolved strains of the fungal pathogen Cryptococcus neoformans show adaptation via heritable transcript level differences specific to mouse MHC haplotype.BMC genomics · 2026Article
- Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis.PLoS genetics · 2026Article
- Deep learning based attention enhanced phylogenetic radial basis function networks (AE-PRBFN) for genomic codon usage classification across species.Scientific reports · 2026Article
185 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
65 authors.
Andrew D YatesEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-8886-4772
James AllenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Ridwan M AmodeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Andrey G AzovEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Matthieu BarbaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Andrés BecerraEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jyothish BhaiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Lahcen I CampbellEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Manuel Carbajo MartinezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Marc ChakiachviliEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Kapeel ChouguleCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Mikkel ChristensenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Bruno Contreras-MoreiraEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Alayne CuzickRothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK.ORCID 0000-0001-8941-3984
Luca Da Rin FiorettoEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Paul DavisEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0001-5545-0824
Nishadi H De SilvaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0003-4802-2375
Stavros DiamantakisEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Sarah DyerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Justin ElserDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Carla V FilippiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Astrid GallEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Dionysios GrigoriadisEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Cristina Guijarro-ClarkeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Parul GuptaDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Kim E Hammond-KosackRothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK.ORCID 0000-0002-9699-485X
Kevin L HoweEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-1751-9226
Pankaj JaiswalDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.ORCID 0000-0002-1005-8383
Vinay KaikalaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Vivek KumarCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Sunita KumariCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Nick LangridgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Tuan LeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Manuel LuypaertEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Gareth L MaslenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Thomas MaurelEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Benjamin MooreEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Matthieu MuffatoEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Aleena MushtaqEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Guy NaamatiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Sushma NaithaniDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.ORCID 0000-0001-7819-4552
Andrew OlsonCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Anne ParkerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Michael PauliniEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Helder PedroEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Emily PerryEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0003-0776-4428
Justin PreeceDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Mark Quinton-TullochEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Faye RodgersWellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Marc RoselloEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Magali RuffierEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-8386-1580
James SeagerRothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK.ORCID 0000-0001-7487-610X
Vasily SitnikEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Michal SzpakEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
John TateEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Marcela K Tello-RuizCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Stephen J TrevanionEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Martin UrbanRothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK.ORCID 0000-0003-2440-4352
Doreen WareCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Sharon WeiCold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
Gary WilliamsEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Andrea WinterbottomEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Magdalena ZarowieckiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Robert D FinnEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0001-8626-2148
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-3897-7955
Funding
Bioinformatics Resource Centers for Infectious Diseases: Tickborne Diseases Activities 75N93019C00077 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI ROOS, DAVID · 2019 to 2023
$30.8MWormBase: a core data resource for C. elegans and other nematodesU24HG002223 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI TIM SCHEDL, PAUL Warren STERNBERG · 2018 to 2026
$18.9MBiotechnology and Biological Sciences Research Council BB/M028372/1Biotechnology and Biological Sciences Research Council BB/P016855/1Biotechnology and Biological Sciences Research Council BB/P024602/1Biotechnology and Biological Sciences Research Council BB/P027849/1Biotechnology and Biological Sciences Research Council BB/S020020/1Biotechnology and Biological Sciences Research Council BB/S02011X/1Biotechnology and Biological Sciences Research Council BB/T015691/1Medical Research Council MR/S000453/1NHGRI NIH HHS U24 HG002223NIAID NIH HHS 75N93019C00077Wellcome Trust 108749/Z/15/ZWellcome Trust 201535/Z/16/ZWellcome Trust 222155/Z/20/Z
Abstract
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.
Indexed as
Databases, GeneticGenomicsInternetSoftwareAnimalsComputational BiologyGenome, BacterialGenome, FungalGenome, PlantPlantsVertebrates
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