Target enrichment sequencing of Rhynchospora tracyi (Sample I4053)
Genomic DNA was extracted using the DNEasy Plant Mini Kit (Qiagen, Valencia, California, USA). The protocol was modified following suggestions (Costa and Roberts 2014) to compensate for frequent low yields obtained with the standard protocol. After extraction, genomic DNA was sonicated to a fragment size of ~300-800 bp using a Covaris E220 Focused-ultrasonicator with Covaris microTUBES. Subsequently, library preparation and indexing were performed on a Beckman-Coulter Biomek FXp liquid-handling robot following a protocol modified from Meyer and Kircher (2010). A size-selection step was also applied after blunt-end repair using SPRI select beads (Beckman-Coulter Inc.; 0.9x ratio of bead to sample volume). Indexed samples were then pooled at approximately equal quantities (typically 16-18 samples per pool), and then each pool was enriched using the Angiosperm v.1 kit (Agilent Technologies Custom SureSelect XT kit ELID 623181). After enrichment, 34 enrichment reactions were pooled in equal quantities for each sequencing lane and sequenced on PE150 Illumina HiSeq 2500 lanes at the Translational Science Laboratory in the College of Medicine at Florida State University