Fish annotation in Ensembl

The actinopterygians, or ray-finned fish, account for nearly half of all extant vertebrates and exhibit a high level of phenotypic diversity. Previous and continuing studies have revealed divergent features of actinopterygian genomes. Specific phenotypes represented in such a diverse group can aid in extricating the set of common genes from those genes that evolved in specific lineages in response to environmental pressures. In order to fuel research into both the evolution of fish and their genome biology we have recently annotated 41 fish species. The Ensembl gene annotation is based on a combination of RNA-seq data (where available), annotation mapping from zebrafish and protein-to-genome alignments using selected UniProt proteins. By generating the annotations in parallel we produce gene sets in a consistent and efficient manner. For species with RNA-seq data we have generated sample-specific RNA-seq gene tracks in addition to generating the main gene set. Depending on the species, the samples may be different tissues, development stages and/or different environmental conditions. These additional gene tracks provide a unique window into the transcriptional profile of the fish, giving indications of what genes are expressing in each sample and also the dominant transcript structure present at each locus. The collection of new fish annotations and other fish genome resources such as updated comparative genomics and variation data will be released in Ensembl version 94 (expected September 2018). Ensembl data is available in a variety of ways including our genome browser at http://www.ensembl.org, Perl and REST APIs, FTP site, publicly accessible MySQL databases and BioMart.