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.