Integrative analysis of chloroplast DNA methylation in a marine alga—Saccharina japonica

Teng, Linhong, Han, Wentao, Fan, Xiao, Zhang, Xiaowen, Xu, Dong, Wang, Yitao, Rahman, Sadequr, Pellegrini, Matteo, Mock, Thomas and Ye, Naihao (2021) Integrative analysis of chloroplast DNA methylation in a marine alga—Saccharina japonica. Plant Molecular Biology, 105 (6). 611–623. ISSN 0167-4412

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Abstract

Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the chloroplast genome because it is predicted to possess a plastid transit peptide.

Item Type: Article
Uncontrolled Keywords: chloroplast genome,dna methylation,photosynthesis,saccharina japonica,agronomy and crop science,genetics,plant science ,/dk/atira/pure/subjectarea/asjc/1100/1102
Faculty \ School: Faculty of Science > School of Environmental Sciences
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Depositing User: LivePure Connector
Date Deposited: 30 Mar 2021 23:45
Last Modified: 04 Apr 2021 02:25
URI: https://ueaeprints.uea.ac.uk/id/eprint/79591
DOI: 10.1007/s11103-020-01113-9

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