GSE185571
Whole-genome DNA methylation landscapes of control and heat-stressed Linum usitatissimum seedlings.
Whole-genome bisulfite sequencing (WGBS) was employed for identification of differential DNA methylation profiles among control and heat-stressed seedlings of a fibre flax (Linum usitatissimum L.) var., JRF-2. It was identified as a tolerant variety of heat stress-induced oxidative damage. High-quality genomic DNA from four samples comprised  3-week-old control and heat-stressed (40±2°C) seedlings, with or without treated with 5-Azacytidine (hypomethylating agent). High-quality and filtered paired-end Illumina reads were aligned to the flax reference genome, assembled in chromosomes, using bwa-meth tool, followed by methylation loci (5-mC) calling using the MethylDackel software. Differentially methylated regions (DMRs) between the control and other samples were identified using the methylKit and annotated using genomation package for their precedence in the promoter/exon/intron/intergenic regions. The DMRs comprised both hyper- and hypomethylated loci, but the latter found dominated due to heat stress in flax seedlings. The WGBS in flax for heat stress will provide a platform to identify epigenetic loci responsible for heat-stress adaptation in flax. Overall design: Total genomic DNA of control and heat-stressed flax (cv. JRF-2) seedlings were quality checked and converted with bisulfite followed by size fractionated and paired-end library constructed. The libraries were sequenced on Illumina HiSeq 2500 using PE 2x150 chemistry. The raw reads were filtered and aligned to the reference genome for 5-mC loci calling using various bioinformatic softwares. A comparative analysis of the methylated loci between control and heat-stressed seedlings identified DMRs from the promoter, exons, introns, and intergenic regions.