AQUA-FAANG
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 |