title: HybSeq with Cyperaceae specific bait kit of Schoenoplectus pungens: mature individual, leaf
design: Genomic DNA was extracted using the QIAGEN DNeasy Plant Mini Kit following manufacturers protocols (QIAGEN, Valencia, CA, USA). Samples were sonicated to a target fragment size of 550 bp using a Covaris E220 Focused-ultrasonicator (Wohurn, MA, USA). Sequencing libraries were prepared using the Illumina TruSeq Nano HT DNA kit (Illumina Inc., San Diego, CA, USA). DNA libraries were checked for quality using the 2100 Bioanalyzer system (Agilent, Santa Clara, California, USA), and library concentration quantied using a Qubit 2.0 Fluorometer (Life Technologies, Grand Island, New York, USA). Indexed samples were pooled in approximately equal quantities, typically 16 samples per equimolar 500-700 ng pool. Pools were enriched using the custom Cyperaceae-specific baits following the manufacturers protocols for the myBaits kit (v3). We used hybridization temperatures of 65C and hybridization times of 24 hours. Paired-end libraries were sequenced on an Illumina MiSeq (2 x 300 bp; 600 cycle v3) at The Field Museum of Natural History (Chicago, IL, USA).