PT  - JOURNAL ARTICLE
AU  - Mahul Chakraborty
AU  - Ching-Ho Chang
AU  - Danielle E. Khost
AU  - Jeffrey Vedanayagam
AU  - Jeffrey R. Adrion
AU  - Yi Liao
AU  - Kristi Montooth
AU  - Colin D. Meiklejohn
AU  - Amanda M. Larracuente
AU  - J.J. Emerson
TI  - Evolution of genome structure in the <em>Drosophila simulans</em> species complex
AID  - 10.1101/2020.02.27.968743
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.02.27.968743
4099  - http://biorxiv.org/content/early/2020/03/15/2020.02.27.968743.short
4100  - http://biorxiv.org/content/early/2020/03/15/2020.02.27.968743.full
AB  - The rapid evolution of repetitive DNA sequences, including heterochromatic regions, satellite DNA, tandem duplications, and transposable elements, can underlie phenotypic evolution and contribute to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented in most contemporary genome assemblies. We generated highly contiguous de novo assemblies for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 years ago. These species diverged from their common ancestor with D. melanogaster ∼3 million years ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive regions in genomes across different evolutionary times. We find a rapid turnover of satellite DNA and extensive structural variation in heterochromatic regions, while the euchromatic gene content is mostly conserved. Despite the overall preservation of synteny, euchromatin of each species has been sculpted by clade and species-specific inversions, transposable elements (TE), satellite and tRNA tandem arrays, and gene duplications. We also find Y-linked genes rapidly diverging, in terms of copy number and recent duplications from the autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.