Abstract
Main conclusion
The rice leaf mitochondrial DNA is more methylated compared to the rice grain mitochondrial DNA. The old rice leaf mitochondrial DNA has also a higher methylation level than the young rice leaf mitochondrial DNA.
Abstract
The presence of DNA methylation in rice organelles has not been well characterized. We have previously shown that cytosine methylation of chloroplast DNA is different between leaf and grain, and varies between young and old leaves in rice. However, the variation in cytosine methylation of mitochondrial DNA is still poorly characterized. In this study, we have investigated cytosine methylation of mitochondrial DNA in the rice grain and leaf. Based on CpG, CHG, and CHH methylation analyses, the leaf mitochondrial DNA was found to be more methylated compared to the grain mitochondrial DNA. The methylation of the leaf mitochondrial DNA was also higher in old compared to young leaves. Differences in methylation were observed at different cytosine positions of the mitochondrial DNA between grain and leaf, although there were also positions with a similar level of high methylation in all the tissues examined. The differentially methylated cytosine positions in rice mitochondrial DNA were observed mostly in the intergenic region and in some mitochondrial-specific genes involved in ATP production, transcription, and translation. The functional importance of cytosine methylation in the life cycle of rice mitochondria is still to be determined.
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Data availability
The data sets generated and analysed during the current study are publicly available in the Gene Expression Omnibus (GEO) database with the Accession Number: GSE115610 in addition to electronic supplementary materials provided here.
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Acknowledgements
The project was funded by School of Science, Monash University Malaysia postgraduate research grant and partly by Malaysian Ministry of Higher Education (MOHE) (FRGS/1/2013/ST04/MUSM/01/1) and Malaysian Ministry of Science, Technology and Innovation (MOSTI) (02-02010-SF0114), respectively. We are thankful to Monash University Malaysia Genomics Facility for the sequencing services and technical assistance. We also express our gratitude to Prof Wickneswari Ratnam, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia for providing the Oryza sativa ssp. indica cv. MR219 seeds.
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KM, experimental design and execution, bioinformatics, and manuscript preparation. SR, QA, BKS, project supervision and manuscript preparation. MHT, bioinformatics and manuscript writing assistance. SS, cytosine methylation analysis of chicken mitochondrial DNA.
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425_2020_3349_MOESM6_ESM.tiff
Supplementary file6 Fig. S1 The visualization of circular rice mitochondrial genome of Oryza sativa ssp.indica cv. 93-11 before and after removal of repeat regions based on BLASTn analysis using GenomeVx webserver. The original 93-11 mitochondrial genome is of 490 kb while the amended 93-11 mitochondrial genome is of 360 kb. The inner and outer circular ring highlights repeat regions in the mitochondrial DNA and the genes integrated from chloroplast DNA, respectively. (TIFF 4237 kb)
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Muniandy, K., Tan, M.H., Shehnaz, S. et al. Cytosine methylation of rice mitochondrial DNA from grain and leaf tissues. Planta 251, 57 (2020). https://doi.org/10.1007/s00425-020-03349-7
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DOI: https://doi.org/10.1007/s00425-020-03349-7