The Challenges of Repetitive DNA in Avian Comparative Genomics

Repetitive DNA sequences are ubiquitous components of genomes and distributed either as tandem repeats (e.g., centromeres, telomeres, microsatellites) or as interspersed repeats (e.g., transposons, endogenous viruses). The recent "big bang" in avian genomics has made a plethora of genome-scale information readily available, however, the study of the impact of repetitive elements on the evolution of birds remains challenging using current techniques for sequencing and genome assembly. Here, I will discuss recent advances in the study of repetitive DNA across the evolution of birds and their closest relatives. Although much of avian repetitive DNA still constitutes genomic "dark matter", there is a growing body of evidence showing long-lasting associations of birds with specific groups of transposons and viruses. Finally, I will demonstrate that state-of-the art approaches are capable of successfully sequencing, assembling, and characterizing "dark matter" in avian genomes.