Annotation of Livestock and Aquaculture species in Ensembl

Ensembl (www.ensembl.org) currently provides integrated genome resources for over 55 vertebrate species, including cow, pig, chicken, horse, tilapia and cod. Sheep is available on our Pre! site. We plan to update the assembly and annotation for chicken on the galGal4 assembly, and produce a complete set of annotation for sheep on the Oarv3.1 assembly in the near future.

Gene annotation in Ensembl is evidenced-based, hence all gene models are supported by protein, cDNA, EST or RNASeq sequence data. Until recently, gene annotation was primarily based on protein sequences with UTRs being supported by cDNAs or ESTs. RNASeq data are becoming an important part of the genebuild process, helping us to generate gene annotation faster and to produce better annotation. RNASeq is useful for providing species-specific evidence for transcription, for annotating UTRs, for filtering the cross-species alignments, and for adding genes not found by cross-species alignments. We currently display RNASeq based gene models for several species, including pig and tilapia. Raw RNASeq alignments are also available and their display provides a useful resource for investigating tissue-specific expression patterns. In addition to gene annotation Ensembl also provides multiple species alignments, gene ortholog relationships and variation annotation.

The data produced by Ensembl is accessible via the web browser, public copies of MySQL databases, and a Perl API. BAM files of the raw RNASeq alignments can be downloaded from our FTP site. Data can be queried through BioMart and using our applications such as the variant effect predictor (VEP). All of Ensembl's code and data are freely available.