Water Stress Responsive Differential Methylation of Organellar Genomes of <i>Zea mays</i>Z59

DNA methylation is an important epigenetic change affecting gene expression in plants in both normal and stress conditions. The organelles, mitochondria and chloroplast play a significant role in sensing and initiating stress response. In this study, we report the methylation pattern in chloroplast and mitochondrial genomes in irrigated and water stressed conditions and its relationship with gene expression of a drought tolerant Zea mays cultivar, Z59. Whole genome bisulfite sequencing was done to analyze the pattern of methylation in both the conditions. Mapping of bisulfite reads to B73 reference of mitochondrial and chloroplast genomes showed hypomethylation in water stressed plants when compared to irrigated plants. Sliding window approach to the methylation count data showed highest peak at 419,800 to 420,800 bp region in mitochondria and at 36,900 to 37,900 bp region in chloroplast genomes in both samples. Annotation of the methylated genomes showed that, genes related to photosystem I & II in chloroplast and nad4 gene in mitochondria were hypo methylated in the water stressed sample. RNA-seq analysis of transcriptomics reads mapped to the same reference showed regulation of rps3, rps2A, ccmFC, atp1 and many uncharacterized genes in mitochondria and psbA, psbD, psbc, psaA, and atpA, genes in chloroplast.