Detection of changes in DNA methylation patterns in Pyropia haitanensis under high-temperature stress using a methylation-sensitive amplified polymorphism assay

DNA methylation is the most important epigenetic regulatory strategy that is involved in various biological processes, including environmental stress response. In the present study, the potential contribution of DNA methylation-mediated gene regulation in a high-temperature-tolerant strain of Pyropia haitanensis (Z-61) was investigated by using the methylation-sensitive amplification polymorphism (MSAP) assay. With high temperature, the level of global DNA methylation (C5-m) in Z-61 decreased from 2.21% (control) to 1.36% (12 h) and 0.60% (144 h). MSAP analysis indicated that the total methylation ratio (%) decreased from 30.19% (control) to 15.82% (12 h) and 16.89% (144 h) and that the demethylation of fully methylated fragments was the main contributor of the DNA methylation alterations. A total of 55 polymorphic bands representing fragments that were generated during methylation/demethylation events in different samples were randomly selected and sequenced, of which 29 fragments were situated within a gene, whereas the others were located within noncoding regions or promoters. The 29 MSAP fragments consisted of 18 fragments that were highly expressed as indicated by RNA-seq analysis and 11 genes that exhibited either very low or no expression at all time points. BLASTN analysis indicated that the methylated fragments situated within genes are homologous to those involved in numerous processes, including abiotic stress response, programmed cell death, photosynthesis, energy metabolism, signal transduction, protein synthesis, and transposon activation. To the best of our knowledge, this is the first report on changes in methylation patterns in macroalgae under environmental stress, and our findings provide insights into the elucidation of the mechanism underlying stress adaptation in P. haitanensis.