<i>Drosophila</i> centromere organization and widespread presence of retroelements at centromeres.

(A) Schematic showing the organization of D. melanogaster centromeres. For at least CenX, Cen4, and Cen3, the bulk of CENP-A chromatin is associated with the centromere islands, whereas the remaining CENP-A is on the flanking satellites. The sequences flanking the Y centromere are not in our assembly, so whether CENP-A is also on satellites is unknown. Although the complexity of island DNA allowed us to identify centromere contigs by long-read sequencing, the flanking satellites remain largely missing from our genome assembly because of their highly repetitive nature. The approximate satellite size estimates are based on Jagannathan and colleagues’ work [25]. (B) Phylogenetic tree showing that centromere-associated retroelements are common across highly diverged lineages: Gossypium hirsutum (cotton) [47], Zea mays mays (maize) [9, 48], Oryza sativa (rice) [49–51], Triticum boeoticum (wild wheat) [52], Cryptococcus [53], Phyllostomid (bat) [54], Hoolock leuconedys (gibbon) [55], Homo sapiens (human) [56] (and a human neocentromere [57]), Macropus eugenii (tammar wallaby) [58–60], Phascolarctos cinereus (koala) [61], and D. melanogaster (this study for endogenous centromeres; also in an X-derived minichromosome [14, 15]). The phylogeny was constructed using TimeTree [62]. Indicated are the retroelement type and the clade that the element belongs to with element types as follows: LTR and non-LTR. The circles indicate the experimental evidence for centromere association of retroelements: FISH, CENP-A ChIP-seq (ChIP), and genome or BAC sequencing (Seq). BAC, bacterial artificial chromosome; CENP-A, centromere protein A; CenX, X centromere; ChIP-seq, chromatin immunoprecipitation sequencing; CRM, centromeric retrotransposons of maize; CRR, centromeric retrotransposons of rice; CRW, centromeric retrotransposons of wheat; FISH, fluorescence in situ hybridization; LAVA, LINE-Alu-VNTR-Alu-like; LINE, long interspersed nuclear element; LTR, long terminal repeat; Mya, million years ago.