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Fig. S1 Microarray validation by RT-PCR.

Fig. S2 Proportion of specific genes from leaf, stem and root organs, separated by overall annotation category.

Fig. S3 Proportion of Arabidopsis thaliana and Populus trichocarpa orthologs with the same pattern of expression (i.e. presence or absence of transcripts) in the two species, in each vegetative organ.

Fig. S4 Rank correlations between expressed genes of Populus trichocarpa Nisqually-1 and Arabidopsis thaliana and between Populus genotypes Nisqually-1 and H11-11 (Populus trichocarpa × Populus deltoides).

Fig. S5 Q-Q plot displaying the distribution of the expression data of orthologs in Populus trichocarpa and Arabidopsis thaliana internodes, nodes, roots, young leaves and mature leaves.

Table S1 Transcriptional unit identified as expressed above background in five tissues (internode, node, root, young leaves and mature leaves), at a false discovery rate of 0.01, 0.05 and 0.10 and the intensity of signal detected relative to control probes (fold-change)

Table S2 Orthologs with the most conserved expression patterns in Arabidopsis thaliana and Populus trichocarpa, in plant nodes and internodes, roots, young and mature leaves, and their Gene Ontology annotation

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