Journal
NEW PHYTOLOGIST
Volume 225, Issue 1, Pages 234-249Publisher
WILEY
DOI: 10.1111/nph.16125
Keywords
brown algae; BS-PCR; DNA methylation; DNMT2; gene expression; life-cycle stages; MeDIP-seq; WGBS-seq
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Funding
- National key research and development program of China [2018YFD0900703, 2018YFD0901503-8, 2016YFC1402102]
- National Natural Science Foundation of China [41676145]
- Shandong key Research and Development Plan [2018GHY115010]
- Qingdao Municipal Science and Technology plan project [17-1-1-96-jch]
- Special Scientific Research Funds for Central Non-Profit Institutes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences [20603022019006, 20603022016001]
- Youth Talent Program - Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao) [2018-MFS-01]
- China Agriculture Research System [CARS-50]
- Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) [2018SDKJ0406-3]
- Ministry of Agriculture and Rural Affairs, China [NFZX2018]
- Taishan Scholars Funding
- Talent Projects of Distinguished Scientific Scholars in Agriculture
- Natural Environment Research Council, UK [NE/R000883/1]
- School of Environmental Sciences at the University of East Anglia, UK
- Region Pays de la Loire
- Nantes Metropole
- NERC [NE/R000883/1] Funding Source: UKRI
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Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.
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