Evolution of bird genomes—a transposon's‐eye view

Birds, the most species‐rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second‐generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird–TE “arms races” has yet to be explored; and (6) upcoming third‐generation genome assemblies suggest that birds exhibit stability in gene‐rich regions and instability in TE‐rich regions. We emphasize that integration of cytogenetics and single‐molecule technologies with repeat‐resolved genome assemblies is essential for understanding the evolution of (bird) genomes.