European Reference Genome Atlas - Pilot Project
The European Reference Genome Atlas (ERGA) is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. With approximately one fifth of the ~200,000 European species at risk of extinction, we need to act fast and together to generate high-quality complete genome resources in large scale.
The Pilot Project, aims to build a pan-European genomics infrastructure that can support the inclusion and equal participation of each European country, at each step of the genome establishment pipeline, from sample collection to publication.
Ensembl is a partner in the ERGA 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) optimised for vertebrates and for non-vertebrates. When a species lacks transrciptomic 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.
| Image | Species | Accession | Annotation method | Annotation | Proteins | Transcripts | Softmasked genome | Repeat library | Other data | View in browser | BUSCO completeness | Alternate haplotype |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Ammodytes marinus | GCA_949987685.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | BUSCO | – |
|
|
Argentina silus | GCA_951799395.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | – | – |
|
Coenonympha glycerion | GCA_963855885.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | – | – |
|
Haliaeetus albicilla | GCA_947461875.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org | BUSCO | – |
|
Mytilus edulis | GCA_963676685.2 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | – | – |
|
|
Silurus aristotelis | GCA_946808225.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org | BUSCO | – |
|
|
Solea solea | GCA_958295425.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | BUSCO | – |
|
|
Thunnus thynnus | GCA_963924715.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | – | – |
|
Trifolium dubium | GCA_951804385.1 | Ensembl Genebuild | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org | – | – |