Nextera mate pair protocol

The genomic library was prepared using the NEBNext DNA Library Prep Kit (New England BioLabs, Ipswich, MA) with an average fragment size of 230 bp. The library was sequenced using 100 bp paired-end reads (PE100) on the Illumina HiSeq 2500 (Illumina, San Diego, CA). A mate-pair genomic library was prepared using the Nextera Mate-Pair Protocol (Illumina) with an average fragment size of 2500 bp, and was paired-end sequenced with 100 bp reads on the Illumina HiSeq analyzer. Ribosomal RNA was removed from total RNA using the RiboMinus Invitrogen Eukaryote kit for RNA (Life Technologies, Carlsbad, CA). The RNA-Seq library was prepared using the NEBNext Ultra RNA Library prep kit (New England BioLabs) with an average fragment size of 250 bp, and was paired-end sequenced with 100 bp reads on the Illumina HiSeq analyzer.

DNA was extracted from adult female L. fabarum in 10 sub-samples (50–100 wasps each) using the QIAmp DNA mini Kit (Qiagen) according to the manufacturer’s instructions, with the inclusion of an overnight tissue digestion at 56 °C. Extracted DNA was then pooled and used to produce Illumina PE and MP, and PacBio libraries. The PE library was prepared using the Illumina Paired-End DNA protocol; the average fragment size was 180 base pairs (bp). The MP library (5 kb insert) was generated with the Nextera mate-pair protocol (Illumina). Both libraries were sequenced on the Illumina MiSeq in Paired-End mode at the Functional Genomics Center Zürich.
Long-read libraries for PacBio RS II sequencing were produced using the DNA Template Prep Kit 2.0 (Pacific Biosciences). Input DNA was mechanically sheared to an average size distribution of 10Kb (Covaris gTube, Kbiosciences) and the resulting library was size selected on a Blue Pippin Size Selection System (Sage Science) machine to enrich fragments >8Kb; quality and quantity were checked on the Bioanalyzer and Qubit, respectively. Ten SMRT Cells were sequenced at the Functional Genomics Center Zürich.