Anopheles funestus pooled template whole genome sequencing of field-collected mosquitoes (Ghana, Benin, Cameroon and Uganda)

Pooled template whole genome sequencing (POOLseq) was carried out, using Anopheles funestus (sensu stricto) mosquitoes. Mosquitoes used in the study were field-caught female mosquitoes from 4 locations in Ghana, Benin, Cameroon and Uganda. In all cases, indoor resting female mosquitoes were collected and used for sequencing. Total genomic DNA was extracted from individual mosquitoes using the QIAgen DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions. Extracted genomic DNA was quantified per individual and combined in equal amounts to form pools (n=40 in all cases). For each pool, whole genome DNAseq libraries were prepared using the TruSeq Nano (Low-Throughput) DNA Library Preparation Kit (Illumina). Libraries were pooled in equimolar amounts (with other libraries not included in this study) and each pool of libraries sequenced on one lane of the HiSeq 2500 (Illumina) at 2x150 bp paired-end sequencing with v4 chemistry.