Long-read sequencing of X. birchmanni populations
We extracted high molecular weight DNA from brain and liver tissue with the NEB Monarch HMW DNA Extraction Kit for Tissue (Catalog #T3060S, NEB, Ipswich, Massachusetts). The purified DNA was size selected for >40kb fragments with the PacBio SRE XL buffer (Catalog #102-208-400, PacBio, Menlo Park, California). Long-read sequencing libraries were then generated by Oxford Nanopore R10.4.1 sequencing. Approximately 3 g of size-selected DNA was prepared with the Oxford Nanopore ligation sequencing kit (Catalong #SQK-LSK114, Oxford Nanopore, Oxford, United Kingdom) following the manufacturers instructions, except we used half volumes of library prep reagents and extended bead elution steps from 5 minutes to several hours at 37 C to allow very long DNA fragments to resuspend completely. We loaded 200-300 ng of prepared library onto a R10.4.1 PromethION flow cell and sequenced on a P2 Solo sequencer with live basecalling with the fastest model enabled. After our targeted sequencing depth was achieved, the data were basecalled again with Guppy v6.4.6 (Oxford Nanopore) using the super-accuracy model.