RT Journal Article SR Electronic T1 Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster JF bioRxiv FD Cold Spring Harbor Laboratory SP 054155 DO 10.1101/054155 A1 D. E. Khost A1 D. G. Eickbush A1 A. M. Larracuente YR 2016 UL http://biorxiv.org/content/early/2016/07/21/054155.abstract AB Satellite DNA (satDNA) repeats can make up a large fraction of eukaryotic genomes. These blocks of tandem repeats are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses genome assembly challenges and has stymied progress on the detailed study of satDNA structure. Here we use single molecule real-time sequencing reads to assemble and study the genomic structure of two complex satDNA loci in Drosophila melanogaster—260-bp and Responder—with unprecedented resolution. We find that complex satDNAs are organized into large tandem arrays interrupted by transposable elements. The homogenized repeats in the array center suggest that gene conversion and unequal crossovers drive the concerted evolution of repeats, the degree to which differs among satDNA loci. Both satDNA arrays have a higher order organization that suggests recent structural rearrangements. These assemblies provide a platform for the evolutionary and functional genomics of satDNAs in pericentric heterochromatin.