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Water Stress Responsive Differential Methylation of Organellar Genomes of Zea mays 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.