Project SummarySeveral compelling questions in genome sequence analysis have been compromised by errorsand gaps in the available genome assemblies. A telomere-to-telomere platinum-quality genomesequence of a human would open doors to investigating many problems associated with geneticdisease and development of platinum-quality model organism genomes will allow earlyexploration of the most efficient ways to pursue these questions. To demonstrate the utility ofmultiple reference-quality genomes we have formulated several questions about genomeevolution that make use of the Drosophila model system. These questions include (1) identifyingnew genes that originated within the Drosophila-specific clade (2) estimating the rates of newgene evolution and examine the variation and constancy of those rates among Drosophilalineages (3) quantifying rates and patterns of divergence of piRNA clusters critical to hostregulation of transposable elements (4) analysis of sequence divergence in heterochromaticrepeats known to play key roles in centromere and telomere function as well as modulatingchromatin states and (5) analysis of Y chromosome gene and loss across the pan-Ychromosome. By obtaining and annotating reference-quality genome sequences of 19Drosophila species spanning 40-60 MY of evolutionary history using an efficient scheme thatcombines deep long-read (PacBio) assembly coupled with targeted sequencing of bacterialartificial chromosomes we will produce a resource that will pave the way for the Drosophilacommunity to tackle pressing hypothesis-driven questions in the field including embryonicdevelopment neurobiology and aging all within a phylogenomics perspective.