Whole Genome Sequencing of Plant DNA

Seeds of PP was germinated, and 15-day-old seedlings were used for genomic DNA extraction using Qiagen DNeasy kit (Qiagen). Qubit 2.0 fluorometer (Thermo Fisher) was used to quantify and NanoDrop 2000 (Thermo Fisher) for quality check of the isolated DNA. The DNA was fragmented to 300 bp size using a Covaris M220 focused ultrasonicator. The fragmented DNA was purified, and sequencing libraries were prepared using Illumina TruSeq DNA sample prep kit (Illumina Inc., United States) as per manufacturer’s specifications. The quantity and size distribution of the libraries were carried out using a Bioanalyzer 2100 (Agilent Technologies). The quantified libraries were subjected for whole genome sequencing on Illumina HiSeq-2000 platform (Illumina Technologies) by paired-end sequencing to generate 90-base pair long, small reads with an insert size of 200–350 bp (Supplementary Figure S2). Standard Illumina pipeline was used to filter the whole genome sequencing data. To remove low-quality reads and reads containing adaptor/primer contamination, FASTQ files were further subjected to stringent quality control using NGS QC Toolkit (v2.3) (Patel and Jain, 2012 (link)).