Ensembl 2024.

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data.

The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has become a cornerstone of the fight against the disease. To support the maximal use of genomic information for SARS-CoV-2 research, we launched the Ensembl COVID-19 browser; the first virus to be encompassed within the Ensembl platform. This resource incorporates a new Ensembl gene set, multiple variant sets, and annotation from several relevant resources aligned to the reference SARS-CoV-2 assembly. Since the first release in May 2020, the content has been regularly updated using our new rapid release workflow, and tools such as the Ensembl Variant Effect Predictor have been integrated. The Ensembl COVID-19 browser is freely available at https://covid-19.ensembl.org.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

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.

Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens.

Accurate and comprehensive annotation of genomic sequences underpins advances in managing plant disease. However, important plant pathogens still have incomplete and inconsistent gene sets and lack dedicated funding or teams to improve this annotation. This paper describes a collaborative approach to gene curation to address this shortcoming. In the first instance, over 40 members of the Botrytis cinerea community from eight countries, with training and infrastructural support from Ensembl Fungi, used the gene editing tool Apollo to systematically review the entire gene set (11,707 protein coding genes) in 6-7 months. This has subsequently been checked and disseminated. Following this, a similar project for another pathogen, Blumeria graminis f. sp. hordei, also led to a completely redefined gene set. Currently, we are working with the Zymoseptoria tritici community to enable them to achieve the same. While the tangible outcome of these projects is improved gene sets, it is apparent that the inherent agreement and ownership of a single gene set by research teams as they undergo this curation process are consequential to the acceleration of research in the field. With the generation of large data sets increasingly affordable, there is value in unifying both the divergent data sets and their associated research teams, pooling time, expertise, and resources. Community-driven annotation efforts can pave the way for a new kind of collaboration among pathogen research communities to generate well-annotated reference data sets, beneficial not just for the genome being examined but for related species and the refinement of automatic gene prediction tools.