Expanding Genomic Annotation Resources For Poultry

As the de facto model bird genome, the chicken occupies a unique and important evolutionary niche and plays a central role in comparative and evolutionary genomics. However, the chicken genome’s coding sequences, intron/exon structures, and potential protein products from each gene in different tissues are not conclusively identified experimentally. We present here Chickspress (http://geneatlas.arl.arizona.edu/), a tissue specific expression atlas for chicken. We are experimentally annotating the chicken genome by directly determining expressed sequences within the genome. Using RNASeq, proteomics and proteogenomic mapping we are analyzing 15 tissues each from two Red Jungle Fowl (male and female) and displaying this on a genome browser. Users are able to view quantitative, tissue-specific expression at both the transcript and protein level. Moreover, we also display novel transcripts identified via RNASeq and novel peptides identified via proteogenomic mapping. Moreover, we are adding a ‘second layer’ of functional annotation information by providing information such tissue specific expression, protein sub-cellular localization and phosphoprotein expression. To support comparative genomics we are also providing a chicken reference gene set and standardized gene nomenclature. We also accept chicken expression data sets from the community and currently have 32 leghorn RNASeq data sets from community submissions using a facile submission interface. We are currently adding more Red Jungle Fowl data sets making the display and visualization of the data easier to use. We expect this resource to provide valuable, experimentally confirmed genomic annotation data for future chicken genome assemblies and will inform genomes from other birds.