Blunt-end, double-stranded libraries were built from 20 μl of DNA extract following Meyer and Kircher (27). The libraries were assessed using real-time quantitative polymerase chain reaction (qPCR). With 1 μl of DNA library, 12.5 μl of 1× Maxima SYBR Green Master Mix, 10.5 μl of dH2O, and 1 μl of each of the 10 μM primers (IS7 and IS8 primers) were ran in duplicates. The libraries were thereafter amplified in five separate PCR reactions with AmpliTaq Gold (Applied Biosystems). PCR products were pooled and cleaned with magnetic beads (Agencourt AMPure XP, Beckman Coulter). We received estimates of the concentration and molarity of the DNA in the cleaned DNA libraries using the 2100 Bioanalyzer Instrument (Agilent Technologies). Consequently, libraries were shotgun-sequenced on Illumina HiSeq 2500 [2 × 125 base pairs (bp), pair-end (PE)] and HiSeq X (2 × 150 bp, PE) platforms at the Science for Life Laboratory (SciLifeLab) facilities in Uppsala (SNP&SEQ Technology Platform, Uppsala University) and Stockholm [National Genomics Infrastructure (NGI) Stockholm]. The base calling was performed using an Illumina CASAVA software, and reads were demultiplexed on the basis of six nucleotide index sequences used in library preparation (27).

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