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.