Plant Molecular Biology

, Volume 100, Issue 1–2, pp 33–46 | Cite as

Comparative sequence and methylation analysis of chloroplast and amyloplast genomes from rice

  • Kanagesswari MuniandyEmail author
  • Mun Hua Tan
  • Beng Kah Song
  • Qasim Ayub
  • Sadequr RahmanEmail author


Key message

Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages.


Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We have characterised the sequence and methylation of grain amyloplast DNA and leaf chloroplast DNA in rice. We have also analysed the changes in methylation patterns in the chloroplast DNA as the rice plant ages. Total genomic DNA from grain, old leaf and young leaf tissues were extracted from the Oryza sativa ssp. indica cv. MR219 and sequenced using Illumina Miseq. Sequence variant analysis revealed that the amyloplast and chloroplast DNA of MR219 were identical to each other. However, comparison of CpG and CHG methylation between the identical amyloplast and chloroplast DNA sequences indicated that the chloroplast DNA from rice leaves collected at early ripening stage was more methylated than the amyloplast DNA from the grains of the same plant. The chloroplast DNA became more methylated as the plant ages so that chloroplast DNA from young leaves was less methylated overall than amyloplast DNA. These differential methylation patterns were primarily observed in organelle-encoded genes related to photosynthesis followed by those involved in transcription and translation.


Amyloplast Chloroplast DNA methylation Tissue specificity Ageing 



This work was supported by the School of Science, Monash University Malaysia postgraduate research grant and in part from grants FRGS/1/2013/ST04/MUSM/01/1 and 02-02010-SF0114 from Ministry of Higher Education (MOHE) and Ministry of Science, Technology and Innovation (MOSTI) of Malaysia respectively. We are grateful to Monash University Malaysia Genomics Facility for the sequencing services and technical assistance. We are also thankful to Prof Wickneswari Ratnam, Universiti Kebangsaan Malaysia (UKM) for providing the Oryza sativa ssp. indica cv. MR219 seeds.

Author contributions

KM carried out the experimental design and bioinformatics analysis, interpreted the results and wrote the manuscript. SR, BKS and QA supervised the research work and assisted with the writing of the manuscript. MHT provided bioinformatics assistance and assisted with the writing of the manuscript. All authors approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 4 (PDF 156 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.School of ScienceMonash University MalaysiaBandar SunwayMalaysia
  2. 2.Tropical Medicine and Biology Multidisciplinary PlatformMonash University Malaysia Genomics FacilityBandar SunwayMalaysia
  3. 3.Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongAustralia
  4. 4.Deakin Genomics CentreDeakin UniversityGeelongAustralia

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