Anopheles merus mate-paired sequences

To identify breakpoints, we performed mate-paired sequencing of the An. merus genome and mapped the read pairs to the An. gambiae AgamP3 genome assembly, which has all standard arrangements. Paired-read sequences that map far apart in the same orientation delineate inversions. Mate-paired genome sequencing was done on DNA isolated from five adult males and females of An. merus. Three libraries of 2 kb, 3kb, and 5 kb were obtained. Mate-paired library preparation and sequencing were performed on the Illumina Genome Analyzer IIx, using 36 bp paired-end processing at Ambry Genetics Corporation (Aliso Viejo, CA, USA).