Genome Resequencing for SNP Identification

SNP identification and genotyping were performed by resequencing of the genome of L. polyactis individuals. Sequencing libraries were constructed following Nunes et al.^{39 (link)} with slight modifications. Genomic DNA of each individual was fragmented into about 350 bp fragments by a Covaris crusher. Sequencing libraries were generated using a TruSeq Library Construction Kit following the manufacturer's instructions. Digested DNA fragments were examined by electrophoresis and were then ligated with barcode adaptors. Ligation products were pooled to select for 350–600 bp fragments using Pippin Prep (Sage Science, USA) after clean up with a QIAquick PCR Purification Kit (Qiagen, Germany). Libraries were enriched by PCR using Phusion® High-Fidelity DNA Polymerase (New England Biolabs, USA). Finally, libraries were cleaned using the QIAquick PCR Purification Kit (Qiagen, Germany) and quantified using the KAPA Library Quantification Kit (Kapa Biosystems, USA) for paired-end sequencing on an Illumina HiSeq™ PE150 platform (Illumina, USA), which produced single-end raw reads of 150 bp.