Repetitive DNA: The Dark Matter of Avian Genomics

Abstract

How much do we really know about bird genomes? Like other eukaryotic genomes, the genomes of birds contain repetitive DNA---tandem repeats, transposable elements, and endogenous viruses. Repetitive regions are notoriously difficult to assemble and often remain inaccessible as gaps within genome assemblies, a situation which may be metaphorically referred to as genomic ``dark matter.'' Here we review avian repetitive DNA from an integrated avian genomics and cytogenetics perspective. While bird genomes are generally relatively repeat-poor, some genomic regions consist almost entirely of repetitive elements. Particularly repeat-rich are centromeres, telomeres, and surrounding regions, as well as the female-specific non-recombining W chromosome. Many of these regions are entirely inaccessible with short-read sequencing but may be much better resolved with long-read sequencing and other single-molecule technologies. We further discuss how repetitive elements may have directly impacted bird speciation through host--parasite arms races, meiotic drive, and changes in genome structure. We conclude with a model for improving genome assemblies and anticipate that the resolution of genomic ``dark matter'' will permit a deeper understanding of bird genomes.