RNA Sequencing of Insect Samples

Samples of first instar larval heads, adult male antennae, and adult female antennae were prepared for RNA sequencing (see Insect Rearing and RNA Extraction; Supplementary Materials and Methods) at the National Genomics Infrastructure sequencing facility (Uppsala, Sweden). RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA) according to the manufacturer’s instructions, with the following changes: the protocols were automated using an Agilent NGS workstation (Agilent, CA, USA) using purification steps as described45 (link)46 (link). Samples were clustered using cBot and sequenced on a HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 2 × 126 setup in RapidHighOutput mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite. The quality scale is Sanger/phred33/Illumina 1.8+.
All sequence read files were delivered to our project account on the UPPMAX Computational Science server (Uppsala, Sweden). For each sample, two fq files were produced, one containing all left-pair reads (sampleX_1.fq) and one containing all right-pair reads (sampleX_2.fq).