AQUA-FAANG

AQUA-FAANG Logo

AQUA-FAANG is a European project that aims to improve understanding of genome function and exploitation of genotype-to-phenotype prediction in the six most important European farmed fish species.

The project brings together world-leading interdisciplinary expertise and industry partners providing direct pathways to commercial exploitation. AQUA-FAANG will functionally annotate the genomes of all six species, employing standardized experimental assays and analysis pipelines defined by the FAANG initiative. Datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre.

Ensembl is a partner in the AQUA-FAANG project, and we annotate the protein-coding and non-coding RNA gene structures using a re-engineered version of our Gene Annotation System (Aken et al, 2017). 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. Data for other species-of-interest for this project, e.g., Danio rerio (Zebrafish), are accessible below.

Species Accession Assembly submitted by Annotation Proteins Transcripts Softmasked genome Repeat library Other data View in browser
Cyprinus carpio GCA_000951615.2 CHINESE ACADEMY OF FISHERY SCIENCE GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Dicentrarchus labrax GCA_000689215.1 MPI-PZ GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Oncorhynchus mykiss GCA_002163495.1 USDA/ARS GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Salmo salar GCA_000233375.4 International Cooperation to Sequence the Atlantic Salmon Genome GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Scophthalmus maximus GCA_003186165.1 CNAG GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Sparus aurata GCA_900880675.1 SC GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Danio rerio GCA_000002035.4 Genome Reference Consortium GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org