Fig. 1

Pattern of vascular bundles along the main floral stem of Brachypodium. a Number of vascular bundles (VB) along the main primary stem of Brachypodium (n = 7). All VBs displayed collateral shape as described in d except in the first internode in which 20% of them were fused with at least one other VB and 14% displayed amphivasal phenotype as showed in e. b Hand-cross section in the fifth internode of WT Brachypodium stem at 45 Days After Germination (DAG). c, Hand-cross section in the first internode of WT stem at 45 DAG. d, Large collateral VB from the fifth internode of Brachypodium stem at 45 DAG. (e) VB with amphivasal phenotype in the first internode of WT Brachypodium stem at 45 DAG. All sections were stained with phloroglucinol-HCl. f Fifth node was used for making cross sections that were then imaged with a confocal microscope. g Eight cross sections illustrate a series of 36 sections (repeated in three different samples) imaged with a confocal microscope (left) and illustration of how VBs were manually identified in different area (right). Within the internode, all VB are distinct from each other. Most small VBs that are represented in pink in the internode are recognizable in the upper leaves as future small veins (green circles). Large vascular bundle colored in orange in the internode are interconnected together in the node (dark blue) and give new VB in the upper internode. Three vascular bundles (red) cross the node without any visible anastomosis. A new vascular bundle (light blue) develops in the node, in front of the axillary bud. h Illustration of stacked typical cross sections in the reconstructed node. i Three-dimensional reconstruction of the internode-node area (748 confocal images were produced for 3D reconstruction). In this reconstruction, VBs are shown in yellow while the three vascular bundles that do not anastomose in the node are shown in red and the neo-formed VB is shown in blue. Each vascular bundle was identified manually with the FreeD software