PacBio Whole Genome Sequencing Protocol

Library preparations and sequencing were performed at Lausanne Genomic essentially as recently described (39 (link)). Briefly, high-molecular weight DNA was sheared with Megaruptor (Diagenode, Denville, NJ, USA) to obtain 10- to 15-kb fragments. After shearing the DNA, size distribution was checked on a Fragment Analyzer (Advanced Analytical Technologies, Ames, IA, USA). A total of 500 ng of DNA was used to prepare a SMRTbell library with the PacBio SMRTbell Express Template Prep kit 2.0 (Pacific Biosciences, Menlo Park, CA, USA) according to the manufacturer’s recommendations. The resulting library was pooled with other libraries which were processed in the same manner. The pool was size-selected with Ampure PacBio beads to eliminate fragments of <3kb. It was sequenced with v2.0/v2.0 chemistry and diffusion loading on a PacBio Sequel II instrument (Pacific Biosciences, Menlo Park, CA, USA) at a 900-min movie length and a pre-extension time of 120 min using one SMRT cell 8 M.