Library Construction and Sequencing
For whole genome resequencing, libraries were built using unique in-line
indexed adapters designed by Rohland & Reich, 2012. First, 100 ng of
DNA per sample were sheared to 400bp on the Covaris E220
focused-ultrasonicator using recommended factory settings for
400bp. Library construction included blunt-end repair, adapter ligation,
and adapter fill-in that followed the protocol by Rohland & Reich,
2012. The individual samples were then PCR amplified with
Pre-hyb primers following Rohland et al., 2015 and PCR products were
purified using bead purification and pooled (Rohland & Reich,
2012). Sample pools were reamplified with indexed Illumina-compatible
primers and they were size selected for fragments between 400-1000 bp
and sequenced at 2x150 on the Illumina NovaSeq 6000 at the
Interdisciplinary Center for Biotechnology Research (ICBR), University
of Florida.