Simplified phenylpropanoid pathway and related genes: A, the expression profiles of selected genes related to the phenylpropanoid pathway. Numbers on the x-axis represent contigs listed in Additional file 3: Table S2. The y-axis represents the FPKM values. B, Common compounds shared by the lignin branch (right) and flavonoids branch (left) are depicted in white. Pathway genes are shown in white boxes (PAL - phenylalanine ammonium lyase; C4H - cinnamate-4-hydroxylase; 4CL - 4-coumarate-CoA ligase; HCT - hydroxycinnamoyl-CoA:quinate shikimatep –hydroxycinnamoyltransferase; C3H-Coumaroyl-CoA 3-hydroxylase; CCoAOMT - caffeoyl-CoA 3-O-methyltransferase; CCR - cinnamoyl-CoA reductase; F5H - ferulate 5-hydroxylase; COMT - caffeic acid:5-hydroxyferulic acid O-methyltransferase; CAD - cinnamyl alcohol dehydrogenase; CHS - chalcone synthase; CHI - chalcone isomerase; F3H - flavonone 3-hydroxylase; DFR - dihydroflavonol 4-reductase; ANS - anthocyanidin synthase).The colored rectangles indicate genes that showed higher levels of expression in E. grandis (red) or in E. urophylla (green).