title: Low coverage WGS of Xiphophorus cortezi x Xiphophorus birchmanni: whole embryo
design: DNA was extracted using the Agencourt DNAdvance magnetic bead-based purification system (Beckman Coulter, Brea, CA) in a 96-well plate format. We followed the recommended protocol for extraction from tissue except that we used half-reactions. Following extraction, DNA was quantified with a BioTek Synergy H1 microplate reader (Agilent Technologies, Santa Clara, CA) and diluted to a concentration of 2.5 ng/ul. We prepared libraries for low-coverage whole genome sequencing using a tagmentation based protocol and the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, San Diego, CA). Briefly, samples were enzymatically sheared and initial adapters were added by incubation with the tagmentation enzyme and buffer at 55C for 5 minutes. Individual i5 and i7 indices were added via a PCR reaction using the OneTaq HS Quick-Load 2X Master Mix (New England Biolabs, Ipswich, MA). Following PCR, samples were pooled and purified using 18% SPRI magnetic beads, quantified with a Qubit Fluorometer (Thermofisher Scientific, Wilmington, DE) and visualized on a Tapestation 4200 (Agilent Technologies, Santa Clara, CA).