Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade

Sproul, J.S., University of Rochester, https://orcid.org/0000-0002-6747-3537

Khost, D.E., University of Rochester, https://orcid.org/0000-0001-6936-8864

Eickbush, D.G., University of Rochester

Negm, S., University of Rochester Medical Center

Wei, X., University of Rochester Medical Center, https://orcid.org/0000-0001-9952-3757

Wong, I., University of Rochester

Larracuente, A.M., University of Rochester, https://orcid.org/0000-0001-5944-5686

john.sproul@rochester.edu, danielle_khost@fas.harvard.edu, alarracu@bio.rochester.edu

Publication date: August 18, 2020

Publisher: Dryad

https://doi.org/10.5061/dryad.2ngf1vhjs

Citation

Sproul, J.S. et al. (2020), Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade, Dryad, Dataset, https://doi.org/10.5061/dryad.2ngf1vhjs

Abstract

ABSTRACTSatellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here we use high-quality genome assemblies to study evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 gm/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spreads by inserting into existing clusters of the older, more abundant 1.688 satellite, in events that were likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher-order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.

Methods

Please see methods here: https://doi.org/10.1101/846238

Usage Notes

This archive includes data files and custom scripts used in our study. We organize the repository by figure number, and include additional directories with scripts and general data files not associated with specific figures.

Funding

National Institutes of Health, Award: R35 GM119515

National Science Foundation, Award: DBI-1811930