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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Actinia mediterranea | GCA_965224875.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:95.6%[S:94.8%,D:0.8%],F:1.7%,M:2.7%,n:3203 | – |
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Ailoscolex lacteospumosus | GCA_965183755.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:95.2%[S:91.7%,D:3.6%],F:3.6%,M:1.2%,n:672 | – |
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Androsace saussurei | GCA_964267185.3 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:87.3%[S:64.9%,D:22.4%],F:7.2%,M:5.5%,n:2805 | – |
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Anisus vorticulus | GCA_964264155.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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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Arca noae | GCA_964261245.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:83.9%[S:82.9%,D:1.0%],F:2.7%,M:13.4%,n:5295 | – |
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Arnica montana | GCA_965212255.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:94.0%[S:81.6%,D:12.4%],F:3.5%,M:2.5%,n:2805 | – |
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Arnica montana | GCA_965212395.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:94.2%[S:81.2%,D:13.0%],F:3.6%,M:2.2%,n:2805 | – |
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Avellara fistulosa | GCA_965178305.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:95.5%[S:92.1%,D:3.5%],F:2.4%,M:2.1%,n:2805 | – |
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Avellara fistulosa | GCA_965178325.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:95.1%[S:91.6%,D:3.5%],F:2.5%,M:2.4%,n:2805 | – |
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Carabus banonii | GCA_964291765.2 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:93.9%[S:93.6%,D:0.3%],F:2.3%,M:3.8%,n:3754 | – |
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Carlina diae | GCA_965177975.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:86.7%[S:81.0%,D:5.7%],F:8.7%,M:4.6%,n:2805 | – |
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Cheirolophus tagananensis | GCA_964300385.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:92.6%[S:87.8%,D:4.8%],F:3.2%,M:4.1%,n:2805 | – |
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Cheirolophus tagananensis | GCA_964300405.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:91.3%[S:88.0%,D:3.3%],F:4.2%,M:4.5%,n:425 | – |
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Cistus crispus | GCA_965213365.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:91.4%[S:84.6%,D:6.8%],F:3.4%,M:5.3%,n:2805 | – |
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Coenonympha oedippus | GCA_964304575.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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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Crocidura zimmermanni | GCA_965212715.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:90.4%[S:88.8%,D:1.6%],F:1.6%,M:8.0%,n:12234 | – |
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Culex laticinctus | GCA_964187845.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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 | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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 | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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 | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:94.6%[S:92.2%,D:2.4%],F:1.7%,M:3.7%,n:3285 | – |
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Cymodocea nodosa | GCA_964274905.3 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:75.5%[S:72.2%,D:3.3%],F:11.3%,M:13.2%,n:2821 | – |
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Dailognatha quadricollis | GCA_965183915.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:94.9%[S:93.8%,D:1.0%],F:1.8%,M:3.4%,n:3754 | – |
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Dendarus foraminosus | GCA_965152765.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:96.1%[S:94.6%,D:1.5%],F:1.2%,M:2.7%,n:2124 | – |
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Deroceras lasithionense | GCA_964271515.3 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:77.2%[S:68.2%,D:9.0%],F:10.6%,M:12.2%,n:4421 | – |
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Erebia palarica | GCA_964035005.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:94.2%[S:93.3%,D:0.9%],F:1.7%,M:4.1%,n:5286 | – |
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Eunicella cavolini | GCA_965177985.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:92.3%[S:91.4%,D:0.9%],F:4.5%,M:3.2%,n:3203 | – |
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Gluvia dorsalis | GCA_964187665.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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 | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:93.6%[S:92.9%,D:0.7%],F:1.6%,M:4.8%,n:5286 | – |
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Graphosoma italicum | GCA_965282445.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:87.3%[S:86.9%,D:0.5%],F:2.8%,M:9.9%,n:3396 | – |
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Graphosoma italicum | GCA_965282455.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:95.7%[S:95.3%,D:0.4%],F:2.9%,M:1.4%,n:3396 | – |
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Hemorrhois hippocrepis | GCA_964340495.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:90.9%[S:88.9%,D:2.0%],F:1.6%,M:7.5%,n:7480 | – |
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Hirudo verbana | GCA_965178055.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:92.4%[S:88.5%,D:3.9%],F:3.9%,M:3.7%,n:672 | – |
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Hirudo verbana | GCA_965178065.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:90.6%[S:87.1%,D:3.6%],F:5.2%,M:4.2%,n:672 | – |
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Lineus lacteus | GCA_965152395.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:96.0%[S:95.8%,D:0.1%],F:2.5%,M:1.5%,n:672 | – |
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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 | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:92.7%[S:86.4%,D:6.3%],F:3.9%,M:3.4%,n:954 | – |
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Martes foina | GCA_964304585.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:95.3%[S:94.5%,D:0.8%],F:0.9%,M:3.8%,n:14502 | – |
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Natrix maura | GCA_964659585.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:93.2%[S:91.4%,D:1.8%],F:1.2%,M:5.6%,n:7480 | – |
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Patella rustica | GCA_965111895.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:95.9%[S:95.4%,D:0.5%],F:1.9%,M:2.2%,n:4421 | – |
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Phorcus turbinatus | GCA_965237135.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:96.4%[S:96.0%,D:0.4%],F:2.5%,M:1.1%,n:4421 | – |
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Phyllidia flava | GCA_964266695.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:88.9%[S:87.5%,D:1.4%],F:2.4%,M:8.7%,n:5295 | – |
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Pinctada radiata | GCA_964261305.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:93.2%[S:92.0%,D:1.2%],F:1.3%,M:5.5%,n:5295 | – |
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Pipistrellus hanaki | GCA_964339955.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | C:94.2%[S:93.0%,D:1.2%],F:0.9%,M:4.9%,n:12234 | – |
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Placobdella costata | GCA_964276725.1 | Ensembl Genebuild | GTF, GFF3 | – | – | – | – | FTP dumps | beta.ensembl.org | C:93.2%[S:91.7%,D:1.5%],F:3.9%,M:2.9%,n:954 | – |
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Prunus ramburei | GCA_965154115.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:94.5%[S:92.7%,D:1.7%],F:2.9%,M:2.6%,n:2805 | – |
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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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Staphylea pinnata | GCA_965153445.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:91.3%[S:82.4%,D:8.8%],F:4.4%,M:4.3%,n:2805 | – |
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Stigmatoteuthis arcturi | GCA_964276865.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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 | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | beta.ensembl.org | 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 | – | – |
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Xanthium orientale | GCA_964271845.3 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:95.0%[S:84.7%,D:10.2%],F:2.8%,M:2.2%,n:2805 | – |
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Xylophaga dorsalis | GCA_965225065.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:95.9%[S:94.4%,D:1.5%],F:2.6%,M:1.4%,n:4421 | – |
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Zelkova abelicea | GCA_965283495.1 | Ensembl Genebuild | GTF, GFF3 | – | – | FASTA | – | FTP dumps | Coming soon! | C:95.2%[S:93.7%,D:1.5%],F:2.2%,M:2.6%,n:2805 | – |