Ion Torrent sequencing of Schizachyrium scoparium ‘The Blues’ genome to develop SSRs and Characterize Little Bluestem core plant collection.
The goal was to produce genome sequences for Schizachyrium scoparium ‘The Blues’  using Ion Torrent PGM sequencing with a 318 chip. DNA was extracted from the little bluestem cultivar ‘The Blues’ using a MO Bio Power Plant Pro DNA Isolation kit (MO Bio Laboratories, Inc., Carlsbad, CA).  A genomic DNA library (400 bp read) was developed for ‘The Blues’ by following the manufacturer’s instructions using the Ion Xpress Plus gDNA Fragment Library Preparation kit (Life Technologies, Carlsbad, CA). After fragment preparation and prior sequencing, the library was quantified using the Ion Library Quantitation Kit (Life Technologies) to determine the appropriate library dilution. Following library dilution, the library was enriched with Ion Sphere Particles using the Ion PGM Template OT2 400 Kit (Life Technologies) in preparation for sequencing. The library was sequenced on the Ion PGM System (Life Technologies) using the Ion PGM Sequencing 400 Kit (Life Technologies) and Ion 318 Chip v2 (Life Technologies). The sequencing reads were assembled into contigs using the default parameters in DNASTAR SeqMan NGen software (DNASTAR, Inc. Madison, WI). Contigs were exported as in FASTA format for microsatellite discovery. A single run generated a total of 681.37 Mb data and 2,654,634 quality reads in a single run. The length of the reads ranged from 50 bp to 450 bp, with an average of 256 bp. All reads were assembled into 8713 contigs with a mean length of 2063 bp.  A total of 2813 SSRs were identified from the contigs and 32.3% of the contigs contained SSRs. Sequences were considered to contain SSRs if they contained a motif 2 to 6 bp in length and the SSR length was at least 12 bp. The most frequent types of SSR were trinucleotide motifs followed by tetranucleotide motifs