Fig. 5
Genes with DE-APA (differential APA site usage) and involved in xylem development. (A) A summary of DE-APA genes identified in our analysis. The number of DE-APA genes exhibiting a shortened 3’ UTR in the transition zone is represented by violet bars, while those exhibiting a lengthened 3’ UTR are represented by green bars. (B) The results of GO (gene ontology) enrichment analysis showed that DE-APA genes were associated with cell wall biogenesis, terpene anabolism, and cis-regulation of gene transcription. The panel (C) shows the variation in the expression of genes with altered 3’ UTRs. The expression value of each sample is calculated as the log2(fold change) of FPKM between the transition zone and sapwood. FC: fold change. (D) shows the expression of DE-APA genes involved in cell wall synthesis, terpenoid biosynthetic and transcriptional regulation. Genes labeled with blue downward arrows have a negative r value (r < 0; these are results of APAtrap analysis), indicating that they might prefer to use shorter 3’ UTR (more proximal poly(A) site) in the transition zone as compared to the sapwood. Similarly, the genes marked with the red upward arrows have a positive r value (r > 0), indicating that they prefer to use longer 3’ UTR (more distal poly(A) site) in the transition zone than sapwood. ‘r’ represents Pearson’s product moment correlation coefficient, \( \in \)[-1,1]. Scale bar on the top of the picture represent log2(FPKM + 1) transformed values. Original FPKM values are shown within the boxes