Signatures of Selection on 48 Bird Genomes Help Detect Functional Regions in the Chicken Genome

Comparative genomics provides a powerful lense to detect regions in multiple sequence alignments which evolve under purifying selection. These so called selectivity constrained elements (CEs) can frequently be associated with biological function. Using recently released bird genomes, made available by the Avian Phylogenetic Consortium, we generated a 49-way EPO low coverage alignment to enhance genome annotation of birds with a focus on the chicken genome. We detected 1.1M CEs covering 19% of the genome, of which only 170k overlap with known protein coding exons. To assign possible function to the remaining 950k CEs we run a series of comparative and functional analyses and established a functional link for a further 195k elements. To detect regions which may function as novel protein coding genes or lncRNAs we run an RNA-seq experiment on 21 chicken tissues, which yielded ~39k novel transcripts. A fraction of these belong to 7,112 novel genes which were classified into 2,895 protein coding and 4,217 lncRNAs and associated with 116k CEs. Some regulatory regions are also known to evolve under selective pressure (e.g. enhancers and transcription factor binding sites). To explore regulatory conservation we run ChIP-seq and CAGE analyses on liver samples and identified 11k and 17k promoter and enhancer associated regions, linked with 24k and 55k CEs, respectively. The greatly enhanced functional annotation, a result of both comparative and functional genomic approaches, greatly benefits basic research, animal breeding and affects the annotation of the relevant bird species included in the study