Repetitive DNA: The Dark Matter of Avian Genomics



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.


Bird evolution Genome assembly Cytogenetics Repetitive element Transposon Virus Centromere Telomere Sex chromosome Speciation 



We thank Anne-Marie Dion-Côté and Cormac Kinsella for helpful discussions and Anne-Marie Dion-Côté, Cormac Kinsella, and Karen Miga for comments on earlier versions of this manuscript. We are also grateful for comments from Robert Kraus and three anonymous reviewers who further improved this manuscript. A.S. was supported by grants from the Swedish Science Foundation (2016-05139) and the SciLifeLab Swedish Biodiversity Program (2015-R14).


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Evolutionary BiologyEvolutionary Biology Centre (EBC), Uppsala UniversityUppsalaSweden
  2. 2.Division of Evolutionary Biology, Faculty of BiologyLudwig-Maximilian University of MunichPlanegg-MartinsriedGermany

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