The repeatome gathers all repeated sequences found either in tandem or as interspersed sequences in the genome. Studies of the repeatome in bird genomes have so far been limited, despite its demonstrated importance in other vertebrate genomes. Indeed, the repeatome is a source of regulation and signalling for gene transcription as well as for the networks controlling some epigenetic marks, and for drivers of ectopic recombination events such as deletions, origination of new genes, functioning of telomeres, etc. This lack of interest in the bird repeatome was likely due to the suggestion that the reduced size of bird genomes was the result of depletions of useless sequences (i.e., non-genic repeated sequences) and the absence of activity of those repeats that were able to amplify by transposition Wicker et al., 2005; Ellengren 2010; Gao et al., 2017. Since publication of the Third Report on Chicken Genes and Chromosomes in 2015 Schmid et al., 2015 new data and analyses have dramatically changed our view of bird genomes, specifically with respect to transposable elements (TEs), GC-rich tandem repeats and their connections to the organization of bird genomes. Unfortunately, repeat annotation of bird genomes continues to be an understudied field. For example, of the four chicken genome models available in 2022 (gal-Gal4-6, Ogye1.0, bGalGal1 GRCg7b and GRCg7w), only galGal4 and 5 have had both interspersed and tandem repeats annotated.
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