Third Report on Chicken Genes and Chromosomes 2015

It is now over 10 years since the first avian genome [International Chicken Genome Sequencing Consortium, 2004] and the first complete avian karyotype [Masabanda et al., 2004] were both published; however, until 2014, avian cytogenetics has focused heavily on descriptive studies [e.g. Griffin et al., 2007, 2008; Skinner et al., 2009; Volker et al., 2010] with less attention to its functional relevance. Last year, however, saw 2 landmark efforts in the chromosomal studies of birds: a special issue of Chromosome Research in April and the announcement of recently completed sequences of multiple new avian genomes in Science and the BMC journals (taking the total number sequenced to over 50) in December. Studying the chromosomes of birds is, perhaps for the first time, telling us more about avian biology, function and evolution than it ever has... Conclusions. The most recent advances in avian cytogenetics have culminated in great promise not only for the study of bird karyotypes, but also for providing insight into the mechanisms of chromosome evolution in general. New avenues for investigation include gene regulation; for instance, it will become necessary to map accurately the physical location of polyadenylation and transcription start sites, important reference points that define promoters and post-transcriptional regulation. It will also become possible to sequence full-length transcripts, to allow accurate identification of alternate splicing events and their controlling elements. The ENCODE (Encyclopedia of DNA Elements) project has helped to define functional elements of the human genome, including those aforementioned as well as other chromatin signals, e.g. active chromatin, enhancers, insulators, methylation domains, etc. An effort of agENCODE is underway to include agriculturally important birds such as chicken, turkey, duck, quail, and perhaps ostrich. The study of cytogenetics will be essential here in helping to define higher-order structures in nuclear organization that show regulatory interactions within and between chromosomes. Finally, reconstruction of evolutionary events allows us to study genome organization and function not only in extant but, by extrapolation, in extinct species also. Reconstruction of avian-reptilian ancestral karyotypes will allow us to define chromosomal rearrangements in long-dead species that have captured the public imagination. Here be dragons!