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.
Highlights
Ensembl Genomes provides access and analysis for non-vertebrate genomes across the domain of life
We provide high-quality annotated genome assemblies, integrate and link with other complementary genome resources, represent genomic diversity and deliver a comprehensive analysis platform [2]
We provide secondary analysis platforms including whole genome pairwise and multiple sequence alignment, homology prediction and transcriptomic analysis, ontology-based gene annotations and pathway associations
Summary
Ensembl Genomes (https://www.ensemblgenomes.org) provides access and analysis for non-vertebrate genomes across the domain of life. It is organised around the five kingdoms of life: plants (https://plants.ensembl.org), invertebrate metazoans (https://metazoa.ensembl.org), fungi (https:// fungi.ensembl.org), protists (https://protists.ensembl.org) and bacteria (https://bacteria.ensembl.org). Our resources are further enhanced by our active collaborations with other major non-vertebrate genome providers including Gramene for plant genomes of crops, models, and species of evolutionary importance [8], VEUPathDB for eukaryotic pathogens [9] and invertebrate vectors of disease-causing pathogens [10], WormBase providing for nematodes and flatworms [11] and PHI-base for manually curated pathogen-host interactions [12]. Genomes provided via Rapid Release, described later, only have a genome browser, minimal functional data imports, BLAST and flat-file access via Ensembl’s FTP site (ftp.ensembl.org/pub/rapidrelease/species/). We highlight the new genomes and features that have been introduced over the last two years
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