Capture, enrichment and sequencing of genic sequences from populations of the grass Festuca ovina from different edaphic microhabitats on the Baltic island of �land
This experiment used a sequence capture assay to capture and enrich genic sequences from populations of the forage grass Festuca ovina that occupied contrasted edaphic microhabitats within alvar grasslands on the Baltic island of �land. A custom Roche NimbleGen SeqCap EZ in-solution capture assay was designed for F. ovina based on transcript sequences from F. ovina and closely related grasses.  It included 102.7 Mbp of genic sequence information, and is likely to cover the majority of genes present in Festuca ovina. Living individuals of F. ovina were recovered from �land in September 2012: 48 plants were recovered from each of four edaphic microhabitats (microhabitat 1 = deep, moist soil with low pH; microhabitat 2 = deep, dry soil with low pH; microhabitat 6 = shallow, dry soil with high pH; microhabitat 7 = shallow, moist soil with high pH). Soil depth, pH and moisture content were measured at the point of plant collection. Collected plants were maintained as clonal lines at Ness Botanic Gardens, Wirral, Cheshire, UK. DNA was extracted from dried leaf tissue using the Qiagen DNeasy Plant kit, following the manufacturers protocol. DNA was extracted from each plant clonal line separately. DNA quality, quantity and integrity were checked via analysis on the nanodrop platform (ThermoFisher Scientific), via qubit assays (ThermoFisher Scientific), and using agarose gel electrophoresis. DNA samples were normalised and pooled to create four pooled samples: one sample representing each of the original microhabitats in the field. The quality and quantity of pooled samples was checked using nanodrop and qubit assays, agarose gels, and the Agilent Fragment Analyzer platform. Festuca ovina gene-associated sequences were enriched from the four pooled DNA samples using the custom assay designed for F. ovina, using the manufacturers protocol (Roche Nimblegen). Quality control of samples, including qPCR, DNA quantitation and fragment length analysis followed the manufacturers protocol. One paired-end Illumina sequencing library was prepared for each pooled enriched sample. These four libraries were combined and sequenced using four lanes of a HiSeq2500 instrument, using 2 x 125 bp paired-end reads. Each pooled sample was represented on each of the four sequencing lanes.