Isofemale line SOU08 from Mayotte
DNA was extracted from single flies flash frozen in liquid nitrogen following QIAamp Mini Kit (Qiagen) protocol without using RNase A. The resulting DNA samples were quantified (Qubit dsDNA HS assay kit, ThermoFisher Scientific), assessed for quality (Nanodrop ND-2000; A260/A280$>$1.8), and stored at 20C. Illumina TruSeq Nano DNA libraries were prepared manually following the manufacturers protocol (TruSeq Nano DNA, RevD; Illumina). Briefly, samples were normalized to 100ng DNA and sheared by sonication with Covaris M220 (microTUBE 50; Sage Science). The samples were end repaired, purified with Ampure XP beads (Agencourt; Beckman Coulter), adaptors adenylated, and Unique Dual Indices (Table) ligated. Adaptor enrichment was performed using eight cycles of PCR. Following Ampure XP bead cleanup, fragment sizes for all libraries were measured using Agilent Bioanalyzer 2100 (HS DNA Assay; Applied Biosystems). The libraries were diluted 1:10 000 and 1:20 000 and quantified in triplicate using the KAPA Library Quantification Kit (Kapa Biosystems). Equimolar samples were pooled, and the libraries were size selected targeting 400-700bp range to remove adaptor monomers and dimers using Pippen Prep DNA Size Selection system (1.5% Agarose Gel Cassette #CDF1510; Sage Sciences). Library pools (24 samples per lane) were run on an llumina HiSeq 4000 platform using the 150bp paired end (PE) Cluster Kit.