Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi

Polyploidy occurs frequently in plants and is an important force in plant evolution and crop breeding. New polyploids face various challenges due to genome duplication and subsequent changes in epigenetic modifications, nucleus/cell size and gene expression. How polyploids produce evolutionary novelty remains to be understood. In this study, a transcriptome comparison between 21-day-old diploid and autotetraploid pak choi seedlings revealed that there are few differentially expressed genes (DEGs), with a greater proportion of DEGs downregulated in response to genome duplication. Genome-wide DNA methylation analysis indicated that the level of DNA methylation is obviously increased, especially in transposable elements (TEs) and 1 kb flanking regions, upon genome doubling. The differentially methylated regions between diploid and autotetraploid pak choi were related to 12,857 differentially hypermethylated genes and 8,451 hypomethylated genes, and the DEGs were negatively correlated with the differential methylation in the regions across the DEGs. Notably, TE methylation increases significantly in regions flanking neighboring non-DEGs rather than those flanking DEGs. These results shed light on the role of DNA methylation in the transcriptional regulation of genes in polyploids and the mechanism of coping with "genome shock" due to genome doubling in cruciferous plants.