Lawrence Berkeley National Laboratory

Genome sequences for most metazoans are incomplete due to the presence of repeated DNA in the pericentromeric heterochromatin. The heterochromatic regions of D. melanogaster contain 20 Mb of sequence amenable to mapping, sequence assembly and finishing. Here we describe the generation of 15 Mb of finished or improved heterochromatic sequence using available clone resources and assembly and mapping methods. We also constructed a BAC-based physical map that spans approximately 13 Mb of the pericentromeric heterochromatin, and a cytogenetic map that positions approximately 11 Mb of BAC contigs and sequence scaffolds in specific chromosomal locations. The integrated sequence assembly and maps greatly improve our understanding of the structure and composition of this poorly understood fraction of a metazoan genome and provide a framework for functional analyses.