European Reference Genome Atlas (ERGA): Biodiversity Genomics Europe (BGE)
The European Reference Genome Atlas (ERGA) is a pan-European initiative with the goal of coordinating the generation of high-quality annotated reference genomes for all eukaryotic biodiversity across the Biogeographic and Marine Regions of Europe. ERGA, as the European node of the Earth BioGenome Project (EBP), aims to scale up the production of genome assemblies and annotations that meet the EBP quality standards. This includes ensuring that the data generated by ERGA Core Projects and ERGA Affiliated Projects are made publicly available and adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) and CARE (Collective benefit, Authority to control, Responsibility, and Ethics) principles.
Ensembl is a partner in the ERGA-BGE project, and we annotate the protein-coding and non-coding RNA gene structures using re-engineered versions of our Gene Annotation System (Aken et al, 2017) optimized for vertebrates and for non-vertebrates. When a species lacks transcriptomic data, we run BRAKER2 to generate hint-guided ab initio gene predictions of protein-coding genes in the default protein mode (see the blog post for more information). After QC, genomes and annotations are made available via our FTP site (see table below) before subsequently being made available in the Ensembl Genome Browser.
The Biodiversity Genomics Europe project is funded by Horizon Europe under the Biodiversity, Circular Economy and Environment (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 22.00173; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy’s Horizon Europe Guarantee Scheme.
| Image | Species | Accession | Annotation method | Annotation | Proteins | Transcripts | Softmasked genome | Repeat library | Other data | View in browser | BUSCO completeness | Alternate haplotype |
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Acomys minous | GCA_964271855.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:97.7%[S:96.7%,D:1.0%],F:0.5%,M:1.8%,n:13798 | – |
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Anisus vorticulus | GCA_964264155.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:94.0%[S:92.9%,D:1.1%],F:1.9%,M:4.1%,n:5295 | – |
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Apodemus agrarius | GCA_964023405.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | – | – |
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Cheirolophus tagananensis | GCA_964300405.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | Coming soon! | C:91.3%[S:88.0%,D:3.3%],F:4.2%,M:4.5%,n:425 | – |
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Coenonympha oedippus | GCA_964304575.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:93.1%[S:92.1%,D:1.0%],F:2.0%,M:4.9%,n:5286 | – |
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Cricetus cricetus | GCA_964304595.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:97.9%[S:96.8%,D:1.1%],F:0.5%,M:1.6%,n:13798 | – |
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Culex laticinctus | GCA_964187845.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:95.5%[S:94.2%,D:1.3%],F:1.4%,M:3.1%,n:3285 | – |
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Culex modestus | GCA_964213205.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:94.1%[S:89.9%,D:4.2%],F:1.4%,M:4.5%,n:3285 | – |
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Culex perexiguus | GCA_964243045.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:94.2%[S:91.2%,D:3.0%],F:1.7%,M:4.1%,n:3285 | – |
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Culex theileri | GCA_964340515.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:94.6%[S:92.2%,D:2.4%],F:1.7%,M:3.7%,n:3285 | – |
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Gluvia dorsalis | GCA_964187665.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:94.8%[S:92.7%,D:2.1%],F:1.6%,M:3.6%,n:2934 | – |
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Graellsia isabellae | GCA_964265105.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:93.6%[S:92.9%,D:0.7%],F:1.6%,M:4.8%,n:5286 | – |
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Malpolon monspessulanus | GCA_964265115.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:88.4%[S:87.0%,D:1.4%],F:2.2%,M:9.4%,n:7480 | – |
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Marifugia cavatica | GCA_964291435.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:92.7%[S:86.4%,D:6.3%],F:3.9%,M:3.4%,n:954 | – |
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Phyllidia flava | GCA_964266695.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:88.9%[S:87.5%,D:1.4%],F:2.4%,M:8.7%,n:5295 | – |
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Placobdella costata | GCA_964276725.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:93.2%[S:91.7%,D:1.5%],F:3.9%,M:2.9%,n:954 | – |
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Rupicapra rupicapra | GCA_963981305.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | – | – |
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Stigmatoteuthis arcturi | GCA_964276865.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:79.3%[S:77.8%,D:1.5%],F:3.2%,M:17.5%,n:5295 | – |
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Tarphius canariensis | GCA_964277315.1 | Ensembl Genebuild | – | – | – | – | – | Check for pre-release files | Coming soon! | C:96.2%[S:95.1%,D:1.1%],F:0.9%,M:2.9%,n:2124 | – |
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Valencia hispanica | GCA_963556495.2 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | – | – |