Profiling dynamics of multi-omics in Arabidopsis whole seeds from Col-0 and Cvi

Genome-wide DNA methylation during Arabidopsis embryogenesis and germination are previously shown in separate sets of reseach. Although it has been known that the change of DNA methylation mainly occurs at CHH context mediated by small RNA-directed DNA methylation (RdDM) pathway during seed ripening and germination, casality of the methylation difference exhibited in natural ArabidopsisArabidopsis ecotypes has not been thoughly studied.Using comparative pairwise multi-omic dynamics in Col-0 and Cape Verde Island (Cvi)-0, we found transcriptome were relatively dynamic in stage-widse whereas DNA methylome were more ecotype-dependent. These ecotype-specific differentially methylated regions (eDMR) are significantly overlap with ecotype-specific 24-nt small RNA clusters (e24sRCs). Col-0-specific regions (Col-0-SR) where Cvi-bisulfite sequencing reads were almost absent were hypermethylated than common regions (CR), that are enriched with TE and structural variantsces (SVs). Col-0-SR Transposable element (TE) are hypermehltyated, longer in size and more pericentromeric. Hypermethylated Col-0-SR showed regional association with copy-gain SVs and e24sRC-Col compared to Cvi-0. Lastly, we show some meiotic crossover-suppressed loci are enriched in Col-SRCol-0-SR exhibiting similar association with e24sRC-Col.