Caenorhabditis elegans mtDNA Duplex-Seq with mutagens

We conducted mutation accumulation line experiments in N2 C. elegans, and two mitophagy deletion strains, dct-1 and pink-1. MA lines were conducted in control conditions, as well as on plates with 50uM of cadmium chloride and 10uM of aflatoxin B1. We performed ultra-sensitive, error-corrected Duplex Sequencing after 50 generations of mutation accumulation in 9-14 MA lines per strain per treatment for a total of 96 mutation accumulation lines sequenced. Libraries were created using standard Illumina prep, with two major variations. First, we ligated Duplex Sequencing adapters (UMIs) during the end repair step of library preparation (Kennedy et al. 2014, Nature Protocols). Second, we conducted a hybridization capture in order to conduct targeted sequencing of just the mitochondrial DNA, following instructions according to the IDT xGen Hybridization protocol.