design: In addition, a whole genome shotgun library was generated with ~500 ng total genomic DNA using the NEBNext Ultra II kit (New England Biolabs). Prior to library preparation, the DNA was sheared to an average size of 600 bp using a Covaris M220 (Covaris). Sequencing was done on a MiSeq apparatus using a 600 cycle v3 kit (2 x 300) at the Plateforme dAnalyses Gnomique (Institut de Biologie Intgrative et des Systmes, Universit Laval, Quebec, Canada), leading to 31.6 million read pairs (19.1 Gb in total)