Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants

Xiao Fan, Wentao Han, Linhong Teng, Peng Jiang, Xiaowen Zhang, Dong Xu, Chang Li, Matteo Pellegrini, Chunhui Wu, Yitao Wang, Michelle Joyce Slade Kaczurowski, Xin Lin, Leila Tirichine, Thomas Mock, Naihao Ye

Research output: Contribution to journalArticle

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Abstract

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.

Original languageEnglish
Pages (from-to)234-249
JournalNew Phytologist
Volume225
Issue number1
Early online date16 Aug 2019
DOIs
Publication statusPublished - Jan 2020

Keywords

  • BROWN ALGA
  • BS-PCR
  • CONSERVATION
  • DIVERGENCE
  • DNA methylation
  • DNMT2
  • DYNAMIC CHANGES
  • GENOME REVEALS
  • METHYLTRANSFERASE HOMOLOG
  • MeDIP-seq
  • PERFORMANCE
  • READ ALIGNMENT
  • RNA
  • WGBS-seq
  • brown algae
  • gene expression
  • life-cycle stages

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