title: Genomic sequencing of combined sample comprising three individual worms: one C. becei strain QG711 female and two C. nouraguensis females (one of strain JU1825 and one of strain NIC59)
design: We prepared Illumina whole genome sequencing libraries as follows. We first transferred each individual to a blank NGM plate with no E. coli lawn for 30 minutes to reduce the amount of contaminating bacterial DNA. We then performed whole genome amplification on each individual using a Qiagen REPLI-g Single Cell kit. Specifically, we picked individual worms into 4 L of PBS sc and froze them at -20 for at least an hour. We thawed the samples and added 3 L of Buffer D2, mixed well, and incubated at 65 for 20 minutes rather than the recommended 10 minutes to aid in worm lysis. The rest of the protocol was performed according to the manufacturers guidelines. We purified the resulting amplified DNA using a Zymo Research Genomic DNA Clean & Concentrator kit (gDDC-10). We submitted approximately 0.5-0.8 ng of each sample to the Fred Hutchinson Cancer Research Centers Genomics Core Facility, who generated a uniquely barcoded sequencing library for each sample using an Illumina Nextera library prep kit, and sequenced those libraries on an Illumina Hiseq2500 to generate 50 bp paired-end reads.