Understanding the functional consequence of selectively constrained regions of the chicken genome

Access to new genome assemblies of birds made it possible to identify regions in bird genomes which are of functional relevance. Regions which show lower level of divergence relative to an assumed neutral standard can indicate the presence of protein-coding genes and exons, regulatory RNAs, transcription factor binding sites as well as enhancer and silencer sequences. Here we present case studies based on our high-resolution map of selectively constrained elements for the chicken genome and how we can potentially link these with functional information.
In our study we created whole genome multiple sequence alignment of 48 birds and using the software GERP++ we called selectively constrained elements. This constraint map was then compared with the current chicken genome annotation and was integrated with 20, tissue specific, RNA-seq dataset.
Currently, less than 4% of the chicken genome is annotated as functional (Ensembl 75) and code for protein-coding and non-coding genes. In comparison we predicted 1.5 million selectively constrained elements, covering approximately 15% of the genome. Relative to the 18,000 transcripts and 17,000 genes present in Ensembl, we predicted over 200,000 transcripts and 50,000 genes based on our RNA-seq study. Several thousands of the new genes are predicted to be protein coding, based on their phylogenetic signatures, while the rest is potentially non-coding and may play a part in regulation. Our study clearly indicates that the functional complexity of the chicken genome is at present poorly understood, but potentially is on par with the mammalian genomes.