Figure S1. Multidimensional scaling analysis of the RNA-seq experiments. Samples are projected on the two first dimensions according to their gene expression profiles. Closeness between samples on the grid indicates a strong similarity. Figure S2. Similar tissue type are strongly correlated. Spearman's rho correlation was measured to check biological replicate homogeneity. Higher rho values indicate stronger similarities between pairs of samples. −log10(Pval) ● 5● 10● 15● 20 OL vs AR YL vs OL YL+YS+OL vs AR copper ion transport ● microtubule−based movement ● cyanate catabolic process ● establishment of protein localization ● DNA unwinding involved in DNA replication ● intracellular distribution of mitochondria ● regulation of root development ● DNA methylation on cytosine within a CG sequence ● carbon utilization ● glutamine biosynthetic process ● maintenance of DNA methylation ● photosystem II assembly ● response to singlet oxygen ● DNA replication initiation ● chlorophyll biosynthetic process ● specification of plant organ axis polarity ● mitotic cell cycle ● reductive pentose−phosphate cycle ● cellular response to nitrogen starvation ● double−strand break repair via homologous recombination ● photosynthesis, light harvesting in photosystem I ● cellular manganese ion homeostasis ● mitotic cell cycle phase transition ● protein−chromophore linkage ● cellular zinc ion homeostasis ● regulation of cyclin−dependent protein serine/threonine kinase activity ● response to light stimulus ● recognition of pollen ● cell division ● photosynthesis ● 0 25 50 75 0 25 50 75 0 25 50 75 transcripts Figure S3. DEG with logFC > 2 mapped to GO biological pathways that are significantly enriched (p<0.05) −log10(Pval) ● 4● 8● 12● 16● 20 OL vs AR YL vs OL YL+YS+OL vs AR microtubule−based movement ● cellular zinc ion homeostasis ● lignin catabolic process ● maintenance of DNA methylation ● response to calcium ion ● plant−type secondary cell wall biogenesis ● DNA methylation on cytosine within a CG sequence ● cellular manganese ion homeostasis ● iron ion transport ● DNA replication initiation ● glutamine biosynthetic process ● iron ion homeostasis ● microtubule−based process ● stomatal movement ● lignin biosynthetic process ● regulation of cyclin−dependent protein serine/threonine kinase activity ● defense response to insect ● cellular response to hypoxia ● mitotic cell cycle phase transition ● cyanate catabolic process ● hydrogen peroxide catabolic process ● mitotic cell cycle ● carbon utilization ● cytoplasmic translation ● methylation ● lipid catabolic process ● plant−type hypersensitive response ● cell division ● plant−type secondary cell wall biogenesis ● response to oxidative stress ● 0 25 50 75 0 25 50 75 0 25 50 75 transcripts Figure S4. DEG with logFC < 2 mapped GO biological pathways that are significantly enriched (p<0.05). logFC>2 regulation of microtubule polymerization or depolymerization ● geranyl diphosphate metabolic process ● fatty acid omega−oxidation ● DNA methylation on cytosine within a CHH sequence ● stomatal complex patterning ● mitotic DNA replication initiation ● leading strand elongation ● female meiotic nuclear division ● chromosome organization ● male meiotic nuclear division ● G1/S transition of mitotic cell cycle ● stomatal complex development ● guard mother cell differentiation ● syncytium formation ● DNA unwinding involved in DNA replication ● DNA methylation on cytosine within a CG sequence ● maintenance of DNA methylation ● pectin catabolic process ● mitotic cell cycle ● DNA replication initiation ● double−strand break repair via homologous recombination ● DNA replication ● nucleosome assembly ● mitotic cell cycle phase transition ● −log10(Pval) regulation of cyclin−dependent protein serine/threonine kinase activity ● ● 5 logFC<(−2) ● 10 cellular response to boron−containing substance levels ● 15 detection of bacterium ● ● YLvsOL 4527 DEG dipeptide transport ● phosphate ion transport ● cellular calcium ion homeostasis ● calcium ion transmembrane transport ● cellular zinc ion homeostasis ● fruit ripening ● response to calcium ion ● negative regulation of stomatal complex development ● phosphorus metabolic process ● cellular manganese ion homeostasis ● glutamine biosynthetic process ● response to carbon dioxide ● phosphate ion homeostasis ● stomatal movement ● xyloglucan metabolic process ● recognition of pollen ● alkaloid metabolic process ● plant−type secondary cell wall biogenesis ● defense response to insect ● cyanate catabolic process ● carbohydrate transport ● carbon utilization ● hydrogen peroxide catabolic process ● 10 20 transcripts Figure S5. Significantly enriched GO biological pathways (p<0.05) in the upregulated (log fold change > 2) and downregulated (log fold change <2) YLvsOL DEG comparison. logFC>2 triterpenoid biosynthetic process ● saponin biosynthetic process ● response to vanadate(3−) ● photosystem I assembly ● regulation of RNA biosynthetic process ● sucrose biosynthetic process ● nonphotochemical quenching ● photosynthetic electron transport in photosystem I ● photosynthetic electron transport in photosystem II ● cyanate catabolic process ● intracellular distribution of mitochondria ● cell fate commitment ● carbon utilization ● abaxial cell fate specification ● photosystem II repair ● photosynthetic electron transport chain ● response to far red light ● cuticle development ● thylakoid membrane organization ● photosystem II assembly ● response to red light ● response to blue light ● chlorophyll biosynthetic process ● −log10(Pval) reductive pentose−phosphate cycle ● photosynthesis, light harvesting in photosystem I ● ● 8 logFC<(−2) ● 12 cellular response to molecule of bacterial origin ● ● 16 regulation of cytokinesis ● ● 20 cellular response to boron−containing substance levels ● OLvsAR 12194 DEG oxaloacetate metabolic process ● fruit ripening ● DNA methylation on cytosine within a CG sequence ● xylan biosynthetic process ● DNA replication initiation ● lignin catabolic process ● xyloglucan metabolic process ● regulation of jasmonic acid mediated signaling pathway ● plant−type secondary cell wall biogenesis ● microtubule−based process ● alkaloid metabolic process ● mitotic cell cycle phase transition ● mitotic cell cycle ● pectin catabolic process ● water transport ● iron ion transport ● regulation of cyclin−dependent protein serine/threonine kinase activity ● iron ion homeostasis ● lignin biosynthetic process ● response to chitin ● hydrogen peroxide catabolic process ● cytoplasmic translation ● 10 20 30 40 50 transcripts Figure S6. Significantly enriched GO biological pathways (p<0.05) in the upregulated (log fold change > 2) and downregulated (log fold change <2) OLvsAR DGE comparison. logFC>2 NA lipid transport ● cytokinin−activated signaling pathway ● response to reactive oxygen species ● starch catabolic process ● cellular response to salt stress ● protein complex oligomerization ● positive regulation of transcription from RNA polymerase II promoter in response to heat stress ● defense response to insect ● sieve element enucleation ● sieve element differentiation ● regulation of cell differentiation ● −log10(Pval) response to chitin ● ● 3 logFC<(−2) ● 4 ● 5 6 YLvsYS 185 DEG ● NA 2.0 2.5 3.0 3.5 4.0 transcripts Figure S7. Significantly enriched GO biological pathways (p<0.05) in the upregulated (log fold change > 2) and downregulated (log fold change <2) YLvsYS DEG comparison. logFC>2 Cytochrome c−type biogenesis ● Cytokinin biosynthesis ● Thiamine biosynthesis ● Chlorophyll catabolism ● Antioxidant ● Cellulose degradation ● Sigma factor ● Porphyrin biosynthesis ● Glycolate pathway ● Oxylipin biosynthesis ● Carbon dioxide fixation ● Carotenoid biosynthesis ● Photoreceptor protein ● Sensory transduction ● Polysaccharide degradation ● 2Fe−2S ● Plastid inner membrane ● Photorespiration ● Alkaloid metabolism ● Isoprene biosynthesis ● Calvin cycle Chlorophyll biosynthesis ● −log10(Pval) Chlorophyll ● Photosystem II ● Photosystem I ● ● ● 5 logFC<(−2) ● 10 Antimicrobial ● 15 DNA integration ● ● Protein phosphatase inhibitor ● Cadmium ● ● 20 YLvsAR 9996 DEG Phosphate transport ● Chitin−binding ● Germination ● Seed storage protein ● Storage protein ● Fruit ripening ● Nodulation ● Aspartyl esterase ● Transposable element ● Vitamin C ● Phenylpropanoid metabolism ● Nitrate assimilation ● Lignin degradation ● Serine esterase ● Pathogenesis−related protein ● Pyrrolidone carboxylic acid ● RNA−directed DNA polymerase ● EGF−like domain ● Lignin biosynthesis ● Hydrogen peroxide Alkaloid metabolism ● ● 0 20 40 60 transcripts Figure S8. Significantly enriched GO biological pathways (p<0.05) in the upregulated (log fold change > 2) and downregulated (log fold change <2) YLvsAR DEG. logFC>2 Inositol biosynthesis ● Cytochrome c−type biogenesis ● Peptide transport ● Chlorophyll catabolism ● Antioxidant ● Glycolate pathway ● Tryptophan biosynthesis ● Carbon dioxide fixation ● Sigma factor ● Glyoxysome ● Carotenoid biosynthesis ● Photoreceptor protein ● Sensory transduction ● EGF−like domain ● Serine protease ● RNA−directed DNA polymerase ● Plastid inner membrane ● Isoprene biosynthesis ● Photorespiration ● 2Fe−2S ● Chlorophyll biosynthesis ● Calvin cycle −log10(Pval) Chlorophyll ● Photosystem II ● Photosystem I ●● ● 5 logFC<(−2) ● 10 Glutamate biosynthesis ● 15 Purine salvage ● ● Calcium/phospholipid−binding ● 3Fe−4S ● ● 20 Hydroxylation ● OLvsAR 12194 DEG Nodulation ● Proteoglycan ● Fruit ripening ● DNA condensation ● Seed storage protein ● Aspartyl esterase ● Allergen ● Phenylpropanoid metabolism ● Storage protein