Chicken Annotation in Ensembl

Chicken is a model organism and farmed animal, with its meat and egg providing an important source of protein for people all around the world. The International Chicken Genome Consortium recently produced an improved reference assembly Gallus_gallus-5.0 (GCA_000002315.3). We have made this available in the Ensembl browser, with data and tools to facilitate research on chicken.

Improvements to the chicken assembly include fewer gaps, longer sequences, more assembled chromosomes, and a better representation of repeat regions. We generated 18,346 protein-coding gene models with the Ensembl Annotation System using publicly available data sets. Two thirds of these models are supported by species specific data coming from cDNAs, Illumina RNA-Seq and PacBio Iso-Seq. We used RNA-Seq data from 21 tissue samples and Iso-Seq data from two tissue samples to annotate untranslated regions (UTRs), alternate transcript isoforms, and 4,636 long intergenic non coding RNAs. Furthermore, we updated the chicken gene names, gene-trees and orthologues, and cross-references to external databases. We also updated our sauropsid and vertebrate multiple whole genome alignments to include the new genome assembly.

These data are available in Ensembl (version e87) and are accessible through our website, www.ensembl.org, our REST API, http://rest.ensembl.org, BioMart (http://www.ensembl.org/biomart ) and our public MySQL server, ensembldb.ensembl.org.

We support the upload and visualisation of data in multiple file format such as BAM or GFF. For groups who wish to share their datasets and view them alongside Ensembl data, we have developed a TrackHubRegistry (http://trackhubregistry.org/) to enable discovery of publicly accessible track data hubs.