Fig. 6
Schematic model of carbon demands during internode development based on transcriptomic analysis. A schematic pathway of carbon import into the developing S. viridis fifth internode, showing the three major demands on carbon supply. A Mapman pathway file (Additional file 4 and Additional file 5) was created to generate this visualisation of gene expression with regard to each carbon demand (also using the updated S. viridis mapping file, Additional file 3, and the experiment file, Additional file 2). Genes were assigned into categories (as labelled on the diagram) and their expression values were displayed as squared log2 fold change from the squared average of the four internode zones for each gene. Up-regulated genes are shown in blue, whilst down-regulated genes are in red. The.mp4 animation (Additional file 6) changes from meristematic zone (a), to cell expansion zone (b), to transition zone (c), to mature zone (d) indicating the internode region with a transparent grey box on the left and highlighting the greatest demand for carbon in each region. MLG mixed linkage glucans, RS raffinose synthase, PDLP plasmodesmata localised proteins, SWEET sugars will eventually be exported transporters, CWI cell wall invertase, HT hexose transporters, PLT polyol transporters, SUT sucrose transporters, CI cytosolic invertases, HK hexokinase, FK fructokinase, FPBase fructose-1,6-bisphosphatase, F6P fructose-6-phosphate, PFK phosphofructokinase, AGPase glucose-1-phosphate adenylyltransferase, UGD UDP-glucose 6-dehydrogenase, UGPase UDP-glucose phosphorylase, G6PI glucose-6-phosphate isomerase, PGM phosphoglucomutase, SPP sucrose phosphate phosphatase, SPS sucrose phosphate synthase, Susy sucrose synthase, TMT tonoplast membrane transporter, CWPS cell wall precursor synthesis, CWP cell wall protein, PAL phenylalanine ammonia-lyase, C4H cinnamate-4-hydroxylase, 4CL 4-hydroxycinnamate CoA ligase, HCT hydroxycinnamoyl transferase, C3H coumarate 3-hydroxylase, CCR cinnamoyl-CoA reductase, CCoAOMT caffeoyl CoA 3-O-methyltransferase, COMT caffeic acid O-methyltransferase, F5H ferulate 5-hydroxylase, CAD cinnamyl alcohol dehydrogenase, CSLA-H cellulose synthase-like A-H, CesA cellulose synthase complex, GT glycosyltransferase, PME pectin methylesterase, PS pectin synthesis, SE sieve element, CC companion cell. Blue and purple dots are representative of sugar flow