As one of the most economically important species and a unique model organism for biological and medical research, the chicken represents the first non-mammalian amniotic species to have its genome sequenced; and so far, the chicken reference genome represents the best assembled and annotated avian genome. Since the release of the first draft genome sequence, the chicken genome assembly has improved greatly in coverage, contiguity and accuracy owing to the continuous efforts made by the chicken genomics community to generate extensive new data using novel sequencing technologies. Transcriptome sequencing, especially the recent effort to characterise full-length transcripts in chicken tissues, has provided key insights into the complexity of structure and function of the chicken genome. In this article, we review the progress in chicken genome assembly and annotation, and recent advances in comparative genomics in birds. Limitations of current data and plans of research are also discussed.