Our knowledge of avian genomes has increased rapidly, starting with the publication of the chicken genome in 2004, a milestone for avian and evolutionary biology. Advances in DNA sequencing now make it possible to produce draft sequences of any vertebrate genome, quickly and cheaply. We have seen the completion of draft genomes of more than 50 other birds, with plans to sequence all 10,000 by the B10K Consortium. With advances in long read sequencing, we are seeing genome assemblies with N50 contigs of more than 3Mb. The annotation of genomes has also been under continuous improvement, taking advantage of transcriptome data generated both by short and long read RNA sequencing technologies. These approaches provide improved gene models, with complex patterns of transcription with multiple RNA isoforms. This has worked well for both coding and non-coding transcripts. Recently, the analysis of 44 bird genomes by the Avian Phylogenomics Consortium opened up new opportunities. For individual species, the sequences coupled with the initial annotations, can serve as a vehicle for basic research. On the other hand generating a multiple genome sequence alignment can enable comparative studies, which benefits all these species. Such studies broaden our understanding of genome evolution and the evolution of traits or can help to disentangle phylogenetic relationships. Our main aim is to analyse the integrated data with a focus on creating a detailed functional map relevant to birds. Such a map can be used to drive the identification of novel protein-coding and non-coding genes, binding sites for transcription factors, enhancers or other functional elements. I will review the current status of avian genome annotation and open up the discussion on future possibilities using phylogenomics in the study of species diversity and the evolution of avian traits.
Supported by BBSRC, EC, Wellcome Trust and University of Edinburgh.