Fosmid Library Preparation and Sequencing

Library preparation of fosmid-DNA was performed using the NEBnext Ultra II FS DNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA) following the manufacturer’s protocol for <100 ng DNA input (30–46 ng input amount). The quality was controlled using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and the libraries were subsequently sequenced on an Illumina MiSeq (Illumina, San Diego, CA, USA) with a 600v3 sequencing kit (2 × 300 bp paired-end reads). The sequence data were trimmed and quality controlled using fastp [30 (link)], and de novo assembled in the CLC Genomics Workbench (version 10; QIAGEN, Hilden, Germany). Sequence annotations were transferred from the reference vector constructs using Geneious Prime (Biomatters, Auckland, New Zealand). The CeHV-2 sequence coverage was above 99% for all sequenced fosmids and sequences were identical to the reference genome (Genbank NC_006560).