ABSTRACT
Highly-repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. The repetitive nature of satDNA poses a challenge for genome assembly and makes progress on the detailed study of satDNA structure difficult. Here we experiment with assembly methods using single-molecule sequencing reads from Pacific Biosciences (PacBio) to determine the detailed structure of two complex satDNA loci in Drosophila melanogaster: the 260-bp and Responder satellites. We optimized assembly methods and parameter combinations to produce a high quality assembly of these previously unassembled satDNA loci and validate this assembly using molecular and computational methods. We find that satDNA repeats are organized into large arrays interrupted by transposable elements. The repeats in the center of the array tend to be homogenized in sequence, though to a different degree for Responder and 260-bp loci. This suggests that gene conversion and unequal crossovers lead to repeat homogenization through concerted evolution, but the degree of concerted evolution may differ among complex satellite loci. We find evidence for higher order structure within satDNA arrays that suggest recent structural rearrangements.