ddRAD-Seq of Actinaria (Entacmaea quadricolor and Stichodactyla spp)
The ddRADseq method following the protocol in Tay et al. (2016) was used with some modifications. 100 ng of DNA from each sample was simultaneously digested with restriction enzymes and ligated to Illumina-compatible adapters. The products were pooled and purified using a 1.2 SeraMag-PEG:DNA ratio. A narrow selection for 400-bp fragments was performed using the PippinPrep and purified. Each pool was assigned a specific Illumina index, and triplicate PCRs were performed per pool to amplify successfully-ligated DNA fragments. Products were pooled, purified and then quantified using the Qubit dsDNA HS Assay kit before combining into a final pool. All libraries were sequenced across three lanes of Illumina Hi-Seq 4000 platform (2  151 bp), with a 40% spike of whole-genome sequencing DNA libraries.