title: Aedes aegypti subspecies Genome sequencing Ox11-male-Thai
design: Deep sequencing libraries were made from pools of Ae. aegypti formosus F1 individuals collected from PK10, Senegal in 2011 and Ae. aegypti aegypti from a rural collection in Pai Lom, Thailand in 2002. Each TruSeq DNA library was prepared using 1 ug of sheared genomic DNA using the manufacturer’s recommended instructions. Libraries were pooled and enriched by exome capture of coding sequences using custom whole transcriptome (Aedes aegypti genome release version 1.3) non-repetitive probes (custom SeqCap EZ Developer probe set (Nimblegen, Roche Life Sciences)) (Supplemental Table 4). In total, 26.7Mb of the genome (20%) was targeted for enrichment. TruSeq libraries were hybridized to the probes, unbound DNA was washed away, and the targeted DNA was eluted and amplified before being sequenced on 2 lanes of a HiSeq2000 (Illumina) for paired-end 2 x 100nt sequencing. TruSeq library preparation, exome capture and sequencing were performed following manufacturer's instructions by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford, UK). Sequencing was done on an Illumina HiSeq 2000, producing reads with quality scores > 30.