Sequencing and assembly was performed by The Genome Institute, Washington University School of Medicine (St. Louis). DNA used for sequencing was derived from Phlebotomus papatasi females from the laboratory of Dr. Mary Ann McDowell, Eck Institute for Global Health, University of Notre Dame (Notre Dame, IN). These sand flies have been through several bottlenecks and were presumed highly inbred. All sequences were generated on the Roche 454 Titanium instrument with the exception of the BAC-ends, which were generated on an ABI3730.