*2.3. Analysis of Differentially Expressed Genes (DEGs)*

Using Bowtie [18], the clean reads were compared to the unigene library. Genes' expression levels were estimated by RSEM (RNA-Seq by Expectation Maximization) [19], and according to the results, the expression abundance of a single gene was expressed as the value of FPKM (transcript fragment per million fragments). The volcano map showed that there were 4829 DEGs, where 3841 (79.54%) were up-regulated and 998 (20.46%) were down-regulated (Figure SA6). Finally, 4165 (85.72%) DEGs were annotated, most of which were annotated to NR (4155) and eggNOG (3957), followed by Pfam (3419), Swissprot (2577), KOG (2426), GO (1756), COG (1554) databases and KEGG (1521) (Table SA3). Clustering results of all DEGs are shown in Figure SA7.

Among the DEGs assigned to KOG and COG, the number of genes in these classes related to plant-resistance of abiotic stress such as "inorganic ion transport and metabolism", "secondary metabolites biosynthesis, transport and catabolism" and "defense mechanisms" were, respectively, 206 (8.50%) and 171 (11.00%), higher than it was for unigenes (Figure 4).

We found that BP, MF and CC accounted for 58.48%, 24.64% and 16.88% respectively by the analysis of 1756 DEGs in GO database. In the entire genetic background and DEGs, the enrichment of genes for each node in the GO database is listed in Figure 5. The top three classes in BP are "DNA integration", "RNA-dependent DNA replication", and "photosynthesis, light harvesting", the most notably of which is the enrichment of "photosynthesis, light harvesting", and the most noticeable of which in MF are the "acyl-CoA dehydrogenase activity" and "oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular"; the *p*-values obtained by the KS test were 0.00024 and 0.00016, respectively. "Ribosome", "fungal-type vacuole membrane" and "nucleus" are the top three in CC, followed up by "photosystem II" and "photosystem I", with *<sup>p</sup>*-values of 8.3 <sup>×</sup> <sup>10</sup>−<sup>5</sup> and 1.4 <sup>×</sup> <sup>10</sup>−<sup>4</sup> . The top five significantly enriched nodes of BP, MF and CC are listed in Table SA4.

The DEGs were distributed to 126 lower pathways of KEGG. The first three pathways with the highest enrichment factor were "photosynthesis antenna proteins", "betalain biosynthesis" and "flavone and flavonol biosynthesis", with factors of 6.84, 6.36 and 4.71, respectively. The top ten most significantly enriched pathways of DEGs in KEGG are listed in Table SA5 . In the "Photosynthesis antenna proteins" pathway, the class with the highest enrichment factor had a total of 20 DEGs, which were all annotated to the homologous gene annotations of "Light-harvesting Chlorophyll a/b Binding (LHC) Proteins"—the apoproteins of the light-harvesting complex of photosystem II (PSII) [20].
