Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila

Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within the Drosophila simulans clade – D. simulans, D. sechellia, and D. mauritiana – and their relative, D. melanogaster. Using chromatin profiling combined with high resolution fluorescence in situ hybridization on stretched DNA, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timesc..., Overview:
This repository contains data and code used in Courret et al. 2024 (https://doi.org/10.1371/journal.pbio.3002911).
CUT&Tag methods: 
We performed CUT&Tag using around 100,000 nuclei per sample. We used the pA-Tn5 enzyme from Epicypher and followed the manufacturer's protocol (CUT&Tag Protocol v1.5). For each species we performed 3 replicates with the anti-CID20 antibody (1:50), one positive control using anti-H3K9me3 (1:100), and one negative control using the anti-IgG antibody (1:100).
For the library preparation, we used the primers in S8 Table of Courret et al. 2024. We analyzed each library on Bioanalyzer for quality control, representative profiles of CENP-A and H3K27me3 profiles are provided in S11B Fig. Before final sequencing, we pooled 2µl of each library and performed a MiSeq run. We used the number of resulting reads from each library to estimate the relative concentration of each library and ensure an equal representation of each library in the final po..., , # Rapid turnover of centromeric DNA reveals signatures of genetic conflict in Drosophila

[https://doi.org/10.5061/dryad.1zcrjdg2g](https://doi.org/10.5061/dryad.1zcrjdg2g)

## Description of the data and file structure

**Overview:**

This repository contains data and code for analysis for Courret et al. 2024 ([https://doi.org/10.1101/2023.08.22.554357](https://doi.org/10.1101/2023.08.22.554357)). In this manuscript, we study centromere evolution in the *Drosophila simulans* clade – *D. simulans*, *D. sechellia*, and *D. mauritiana* – compared to their relative, *D. melanogaster*. We use chromatin profiling (CUT&Tag) combined with high resolution fluorescence in situ hybridization on stretched DNA, and evolutionary analyses to  characterize and compare all centromeres across these species.

**CUT&Tag:** 

We performed CUT&Tag using around 100,000 nuclei per sample. We used the pA-Tn5 enzyme from Epicypher and followed the manufacturer's protocol (CUT&Tag Protocol v1.5)....