WGS of Arabidopsis lyrata
Total genomic DNA was extracted from fresh leaves using NucleoSpin Plant II kit (Macherey-Nagel). The DNA was fragmented with Bioruptor sonication system (Diagenode), after which the libraries for Illumina whole-genome sequencing were prepared with NEBNext master mix kit (New England Biolabs). We first removed low quality reads and Illumina adapters with Trimmomatic. The reads were aligned to A. lyrata v1.0 reference genome with bwa-mem. Duplicated reads were removed with Picard tools and indels realigned with GATK.