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

journal contribution
posted on 2019-05-01, 00:00 authored by K Muniandy, Mun Hua Tan, B K Song, Q Ayub, S Rahman
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. Abstract: 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.

History

Journal

Plant molecular biology

Volume

100

Issue

1-2

Pagination

33 - 46

Publisher

Springer

Location

Dordrecht, The Netherlands

ISSN

0167-4412

eISSN

1573-5028

Language

eng

Publication classification

C1 Refereed article in a scholarly journal

Copyright notice

2019, Springer Nature B.V.