Genome Skimming for Genetic Diversity Analysis

The genetic diversity analysis of I. cangae individuals was performed using the genome skimming approach (Figure 2a) (Malé et al., 2014 (link); Weitemier et al., 2014 (link); Wessinger et al., 2018 (link)). Shotgun paired‐end libraries were constructed from 50 ng of isolated DNA. For that, samples were subjected to a random enzymatic fragmentation in which the DNA was simultaneously fragmented and bound to adapters using the QXT SureSelect kit (Agilent Technologies). The fragmented DNA was purified using AmPure XP beads (Beckman Coulter) and subjected to an amplification reaction using primers complementary to the Illumina flowcell adapters. Amplified libraries were again purified using AmPure XP beads (Beckman Coulter), quantified using the Qubit 3.0 Fluorometer (Thermo Fisher Scientific Inc.), and checked for fragments size in the 4,200 TapeStation (Agilent Technologies®) using a ScreenTape DNA 1,000 kit (Agilent Technologies). The libraries were adjusted to a 4 nM concentration, pooled, denatured, and diluted to a running concentration of 1.8 pM. The sequencing run was performed in the NextSeq 500 Illumina platform using a NextSeq 500 v2 kit high output (300 cycles).