Fig. 4

Poly-A selected RNA read abundance of nuclear genes with homology or annotation suggesting organellar transfer (a. and b.), and organellar encoded genes (c.) aligned to the nuclear genome only (blue) and the nuclear and organellar genomes of E. grandis (green). a. Variance stabilizing transformation (VST) counts of 141 organellar transferred genes in the nuclear genome of polyA selected RNA sequencing data aligned to the nuclear genome of E. grandis only. b. VST counts of full-length transferred genes in the nuclear genome of polyA selected RNA sequencing data aligned to the nuclear and organellar genomes of E. grandis simultaneously. c. VST counts of organellar encoded genes of polyA selected RNA sequencing data aligned to the nuclear and organellar genomes of E. grandis simultaneously. Row dendrograms on the left-hand side of all three heat maps show clustering of genes based on expression variation between tissues. Tissue samples are shown at the bottom edge of each heatmap, three biological replicates per tissue. Tissues are abbreviated as follows: Mature leaf (ML), young leaf (YL), shoot tips (ST), flowers stage 1 (FL_1), flowers stage 2 (FL_2), flowers stage 3 (FL_3), immature xylem (IX), and phloem (PH). The range of VST count values per heatmap are represented from low (white) to high (blue) for the polyA selected RNA mapping to the nuclear genome only, and from low (yellow) to high (green) for the polyA selected RNA mapping to the nuclear and organellar genomes. The bar on the right of the heatmaps shows the organellar origin of each gene, either plastid (transferred or encoded- green) or mitochondrial (transferred or encoded- blue)