Leaves had the most DEGs: 5136, of which 53.3% were upregulated and 47.7% were downregulated. Hypocotyls had 653 DEGs, of which 35.4% were upregulated and 64.6% were downregulated. Roots had only 29 DEGs, of which 27.6% were upregulated and 72.4% were downregulated (Fig. 7).
Overall, the organs shared few DEGs (Fig. 8). Many DEGs in leaves and hypocotyls were potentially related to cold stress (Table S7). In leaves, this was the case for histone and heat shock proteins genes (115 and 75 genes, respectively). Interestingly, 108 of the 115 histone genes were upregulated. Other genes potentially related to cold stress included lipases, germin-like proteins, glycine-rich proteins and LEA proteins were detected. No gene related to the ICE-CBF-COR cascade was differentially expressed. In hypocotyls, many genes were related to the biosynthesis of lipids (e.g., lipases, acyltransferases, very-long-chain 3-oxoacyl-CoA synthases) or cutin, suberin and wax (e.g., casparian strip proteins, fatty acyl-CoA reductases, plant lipid transfer proteins) (41 and 29 genes, respectively). Other genes potentially involved in cold stress included proline-rich and glycine-rich cell-wall proteins and expansins. Even in this case, no gene related to the ICE-CBF-COR cascade was differentially expressed.