The m6A epitranscriptomic landscape of Setaria viridis and the domesticated foxtail millet (S. italica)

However, the evolution and roles of m6A modifications in plant domestication remain largely unexplored. This study combined RNA-seq and MeRIP-seq data to compare m6A modifications profiles between foxtail millet (Setaria italica, Yugu1) and its wild ancestor S. viridis (A10).

Peak calling analysis identified 6,928 m6A peaks associated with 6,407 protein-coding genes in Yugu1 and 6,274 m6A peaks in 5,858 genes in A10, respectively. Comparative analysis revealed numerous differentially expressed genes (DEGs) and differentially methylated peaks (DMPs), whose functions were elucidated by GO and KEGG enrichment analyses. Integration of DMPs paired with DEGs, we found 209 hyper-methylated peaks associated with upregulated transcription levels, and 90 hypo-methylated peaks associated with downregulated transcription levels.