Centromeres are enriched in non-LTR retroelements in the <i>Jockey</i> family.

(A) Density of all repetitive elements on each candidate centromere contig and the entire genome (minus the centromeres) grouped by type: non-LTR retroelements, LTR retroelements, rDNA-related sequences, and simple satellites. G2/Jockey-3 is present on all centromeres. An * indicates annotations based on similarity to retroelements in other Drosophila species: Gypsy-2 is from D. simulans, Gypsy-24 and Gypsy-27 are from D. yakuba, and Gypsy-7 is from D. sechellia. For annotation, see Dryad repository file 9: https://doi.org/10.5061/dryad.rb1bt3j [37]. The underlying data can be found in S1 Data. (B) Maximum-likelihood phylogenetic tree based on the entire sequence of all G2/Jockey-3 copies in D. melanogaster inside (squares) and outside (circles) of centromeric contigs and on the consensus repeat in its sister species D. sechellia and D. simulans and a more distantly related species (D. yakuba). The tree shows that centromeric G2/Jockey-3 elements do not have a single origin (see Dryad repository files 13 and 15: https://doi.org/10.5061/dryad.rb1bt3j [37]). Cen2, centromere 2; Cen3, centromere 3; Cen4, centromere 4; CenX, X centromere; CenY, Y centromere; ETS, external transcribed spacer; IGS, intergenic spacer of the ribosomal genes; ITS, internal transcribed spacer; LTR, long terminal repeat; Prodsat, Prod satellite; TART, Telomere-associated retrotransposon.