Genomic DNA Extraction and Sequencing of Limonium

Genomic DNA was extracted from liquid nitrogen grounded leaves of all samples collected for this work using the kit “innuPREP Plant DNA Kit” (Analytik Jena AG) with the SDS based Lysis Solution OPT protocol, which produced the best results for Limonium species. DNA was quantified in Qubit 2.0 (Invitrogen) using Qubit dsDNA HS Assay kit, quality checked using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, United States), and integrity verified using agarose gel electrophoresis (1%). Isolated DNA samples with a minimum concentration of 30 ng/μl were sent to Elshire GBS services (The Elshire Ltd., Manawatu, New Zealand) to perform library preparation and sequencing. Library preparation for deep sequencing was carried out using the TruSeq Nano DNA Library Preparation Kit (350 bp insert size). The genotyping-by-sequencing data was generated following the method described in [26 (link)] and included the following changes: 100 ng of genomic DNA were used, 3.6 ng of total adapters were used, genomic DNA was restricted with ApeKI enzyme and the library was amplified with 18 PCR cycles. Sequencing of Limonium cDNA libraries was carried out using the Illumina HiSeq Ten platform with 2 × 150 bp paired end reads.