The supposed nature of each isolate (i.e. S. haematobium; S. bovis or hybrid) was first validated based on a classical genotyping at the mitochondrial COI and at the ITS2 nuclear gene [18,26,27]. Individual genomic libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina). One nanogram of genomic DNA was used as the template for each individual sample. Libraries were cleaned using 90 μL of AMPure XP beads (Beckman Coulter) to enrich libraries with fragments ranging from 300 to 500 bp. The quality of each library was then assessed using Agilent Technology 2011 Bioanalyser with a High Sensitivity DNA chip as recommended in the protocol. Individual libraries were sent to the Bio-Environment platform (University of Perpignan) where they were normalized and pooled before being paired-end sequenced within two independent runs (2x150 bp) on a NextSeq 550 (Illumina).

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