GO enrichment analysis of DEGs
Up-regulated genes and down-regulated genes were divided into four classes of DEGs. For each of the four groups of down-regulated genes, a Venn diagram was created. The results showed that there were 1617 down-regulated genes in WT, gun1 , SALK_047877 ,SALK_083115, and 322 down-regulated genes in the mutants only (Figure 6a). GO enrichment analysis of the 322 down-regulated genes in the mutants revealed that they were mainly enriched in the response to fatty acids, in nucleobase transport, toxin metabolic processes, regulation of defense response, and plant hormone signal transduction, (Figure 6b). For each of the four groupings of up-regulated genes, Venn diagrams were created. The analysis indicated 373 up-regulated genes in WT, gun1 , SALK_047877 , and SALK_083115 , 185 up-regulated genes in the mutants only, and 2688 up-regulated genes in WT only (Figure 6c). GO enrichment analysis of the 185 up-regulated genes in the mutants showed that they were mainly enriched in tetrapyrrole metabolism, ribosome components, cytokinin signaling, embryo development, and photosynthesis (Figure 6d). GO enrichment analysis of the 2688 up-regulated genes in WT revealed that they were mainly enriched in the response to salicylic acid, vesicle-mediated transport, autophagy, autophagosome organization, and salicylic acid-mediated signaling pathway (Figure 6e).
GO enrichment analysis of plastid-related DEGs
A comparison of chloroplast and mitochondrial DEGs for the LIN versus (vs) control comparison revealed differences. GO enrichment analysis revealed that most down-regulated mitochondria-related DEGs ingun1 , SALK_047877 , and SALK_083115 were enriched in the generation of precursor metabolites and energy, carbon metabolism, NADH metabolic process, and amino acid metabolic processes (Supplementary Figure 3a). Up-regulated mitochondria-related DEGs ingun1 , SALK_047877 , and SALK_083115 were mainly enriched in valine, leucine, and isoleucine degradation, amino acid catabolism, mitochondrial transmembrane transport, and reactive oxygen species (Supplementary Figure 3b). Down-regulated and up-regulated chloroplast-related DEGs were enriched in similar GO terms ingun1 , SALK_047877 ,SALK_083115, and WT seedlings, such as the response to cold, biosynthesis of amino acids, starch metabolic processes, photosynthesis, carbon metabolism, biosynthesis of amino acids (Supplementary Figure 3c-d). However, protein import into chloroplast stroma was only enriched in WT (Figure 6c). These findings indicate that the effect of LIN treatment on the expression of chloroplast-related genes is similar in both mutant and WT seedlings, although the magnitude of the effect of LIN on mutants and WT seedlings differs to some extent.