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 carpio GCA_905221575.1 WAGENINGEN UR GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Dicentrarchus labrax GCA_905237075.1 Hellenic Centre for Marine Research, Institute for Marine Biology, Biotechnology and Aquaculture, Heraklion, Crete, Greece GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Oncorhynchus mykiss GCA_013265735.3 USDA/ARS GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Salmo salar GCA_905237065.2 NORWEGIAN UNIVERSITY OF LIFE SCIENCES GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Scophthalmus maximus GCA_013347765.1 CIGENE GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Sparus aurata GCA_900880675.1 SC GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org
Danio rerio GCA_000002035.4 Genome Reference Consortium GTF, GFF3 FASTA FASTA FASTA Repeatmodeler FTP dumps ensembl.org