Genomic DNA Extraction and Sequencing of Nematodes

To extract DNA, we transferred nematodes from three recently starved 10 cm NGMA plates originally spotted with OP50 E. coli into a 15 ml conical tube by washing with 10 ml of M9. We then used gravity to settle animals in the conical tube, removed the supernatant, and added 10 ml of fresh M9. We repeated this wash method three times to serially dilute the E. coli in the M9 and allow the animals time to purge ingested E. coli. Genomic DNA was isolated from 100 to 300 µl nematode pellets using the Blood and Tissue DNA isolation kit (cat no. 69506, Qiagen) following established protocols (Cook et al., 2016 (link)). The DNA concentration was determined for each sample using the Qubit dsDNA Broad Range Assay Kit (cat no. Q32850, Invitrogen). Sequencing libraries were either generated with KAPA Hyper Prep kits (Kapa Biosystems), Illumina Nextera Sample Prep Kit (Illumina, Inc.), or New England BioLabs NEBNext Ultra II FS DNA Library Prep (NEB). Samples were sequenced at the Duke Center for Genomic and Computational Biology, Novogene, or the Northwestern Sequencing facility, NUSeq. All samples were sequenced on the Illumina HiSeq 4000 or NovaSeq 6000 platform (paired‐end 150 bp reads). The raw sequencing reads for strains used in this project are available from the NCBI Sequence Read Archive (Project PRJNA549503).