Fig. 2
CPL3 profoundly affects flg22-triggered alternative splicing events. A CPL3 plays a more important role in flg22-triggered DASs than flg22-triggered DEGs. Venn diagram shows the percentage and gene numbers between up-/downregulated flg22-DEGs (top) and flg22-DASs (bottom) in WT and cpl3-3. The flg22-DEGs were identified based on (|FC|) ≥ 2 and FDR < 0.01. The flg22-DASs were selected based on |ΔPS|≥ 0.1 and FDR < 0.01. B CPL3 regulates isoform-switched DASs. The isoform-switched DASs were identified when a pair of transcripts reversed their relative abundance between mock and flg22 treatments. A Venn comparison plot illustrates the overlap of isoform-switched DASs between WT and cpl3-3 in response to flg22 treatment. C–E Correlation analyses of flg22-DEGs, flg22-DTUs, and flg22-DASs between WT and cpl3-3. The gene expression changes or proportional isoform usages from CPL3-dependent flg22-DEGs (C), flg22-DTUs (D), and flg22-DASs (E) were represented as green, orange, and blue dots with trend lines, respectively. The gene expression changes or proportional isoform usages from CPL3-independent flg22-DEGs, -DTUs, and -DASs were represented as black dots with trend lines. The log2(FC) values were used for flg22-DEGs and flg22-DASs, and the ΔPS values were used for flg22-DTUs. The X-axis and Y-axis values are from WT or cpl3-3, respectively. The trend line equation and the Pearson correlation coefficiencies (R2) between WT and cpl3-3 were labeled. The correlations were analyzed by the Chow test between CPL3-dependent and -independent flg22-DEGs, flg22-DTUs, and flg22-DASs. Non-statistically (ns) and statistically significant differences with p values were indicated in the figure. F GO analysis using 687 of CPL3-dependent flg22-DASs. The statistically enriched gene ontology terms were identified based on the frequency of CPL3-dependent flg22-DASs annotated to their frequency in the genome with the cut-off of fold enrichment ≥ 1 and false discovery rate (FDR) < 0.05. G The total number of flg22-triggered AS events in CPL3-dependent (CPL3-dep) and CPL3-independent (CPL3-indep) flg22-DTUs. The different types of AS events, namely alternative 3′ splicing (A3S), alternative 5′ splicing (A5S), intron retention (IR), and exon skipping (ES), were depicted as red, orange, green, and blue bars, respectively. H The distribution of flg22-triggered AS events in CPL3-dependent and CPL3-independent flg22-DTUs. The number of flg22-triggered AS events across 5′-leader, CDS, and 3′-tailer is indicated by red and blue lines for WT and cpl3-3, respectively. The relative position was calculated as the average of the alternative coordinates of the AS event, scaled by the length of the CDS, and then converted to a percentage based on their full lengths, dividing into 10% windows. The position of the ATG start codon and stop codon are indicated by black dashed lines, separating the 5′-leader and 3′-tailer from the CDS. I Relative isoform abundances of three representative CPL3-dependent flg22-DASs in WT and cpl3-3. The isoform usage (IU) was calculated by the percentage abundance of a transcript compared to the total transcripts of the gene. The β and α represent constitutive and alternative splicing isoforms, respectively. The absolute ΔPS values (in parentheses) and FDR values between mock (white bar) and flg22 treatment (black bar) are indicated at the top of each comparison. Non-statistically significant comparisons (ns) were indicated as gray. The expression levels of individual transcripts were retrieved from RNA-seq data