genotype-by-sequencing of 6 Alpheus snapping shrimp
Genomic DNA was extracted from 24 individuals using the DNeasy tissue kit (Qiagen Inc., Valencia, California), and samples were treated with RNase following the manufacturers protocol. Three to four replicate GBS libraries per individual were optimized, generated, and sequenced at the Cornell University Biotechnology Resource Center Genomic Diversity Facility following the protocol of (Elshire et al. 2011), resulting in a total of 96 samples. Briefly, genomic DNA was digested with EcoT22I (A|TGCAT) and barcoded adapters were ligated onto resulting restriction fragments. Pooled libraries were sequenced on a single Illumina HiSeq 2000/2500 lane, obtaining 100 base pair, single-end sequencing reads. Sequence reads from replicate libraries were combined.