Data from: Islands of retroelements are major components of Drosophila centromeres

Centromeres are essential chromosomal regions that mediate kinetochore
assembly and spindle attachments during cell division. Despite their
functional conservation, centromeres are amongst the most rapidly evolving
genomic regions and can shape karyotype evolution and speciation across
taxa. Although significant progress has been made in identifying
centromere-associated proteins, the highly repetitive centromeres of
metazoans have been refractory to DNA sequencing and assembly, leaving
large gaps in our understanding of their functional organization and
evolution. Here, we identify the sequence composition and organization of
the centromeres of Drosophila melanogaster by combining long-read
sequencing, chromatin immunoprecipitation for the centromeric histone
CENP-A, and high-resolution chromatin fiber imaging. Contrary to previous
models that heralded satellite repeats as the major functional components,
we demonstrate that functional centromeres form on islands of complex DNA
sequences enriched in retroelements that are flanked by large arrays of
satellite repeats. Each centromere displays distinct size and arrangement
of its DNA elements but is similar in composition overall. We discover
that a specific retroelement, G2/Jockey-3, is the most highly enriched
sequence in CENP-A chromatin and is the only element shared among all
centromeres. G2/Jockey-3 is also associated with CENP-A in the sister
species Drosophila simulans, revealing an unexpected conservation despite
the reported turnover of centromeric satellite DNA. Our work reveals the
DNA sequence identity of the active centromeres of a premier model
organism and implicates retroelements as conserved features of centromeric
DNA.