**Figure 4.** The 20 most abundant Kyoto Encyclopedia of Genes and Genomes pathways (**A**) and 10 most abundant Gene Ontology classifications (**B**) of differentially expressed genes after exposure to mixtures of BDE-47 and nickel treatments. Nuclear outer membrane-endoplasmic reticulum membrane network: ERMN; endoplasmic reticulum: ER; proton-transporting two-sector ATPase complex, proton-transporting domain: PTTS; ligase activity, forming carbon-nitrogen bonds: FCNB; ligase activity, forming carbon-oxygen bonds: FCOB; oxidoreductase activity, acting on the aldehyde or oxo group of donors: AorOXO.

**Figure 5.** Heatmap of differentially expressed genes involved in photosynthesis and nitrogen metabolism that responded to exposure to mixtures of BDE-47 and nickel. Only genes with |log2 fold| changes > 2 and *p* < 0.05 after 48 h and/or 72 h are shown.

A total of 14 DEGs were involved in nitrogen metabolism (Figure 5B, Table S7). Among these, 12 genes exhibited increased expression after exposure to mixtures of BDE-47 and nickel. *PHATRDRAFT\_8155* (nitrite reductase), *PHATRDRAFT\_13154* (Pyr\_redox\_2), *PHA-TRDRAFT\_26029* (MFS\_1), and *PHATRDRAFT\_54983* (FAD\_binding\_6) exhibited very high expression levels with log2-fold changes >5 (Figure 5B, Table S7). Thus, nitrogen metabolism might be enhanced by exposure to mixtures of BDE-47 and nickel.

#### *3.7. DEGs Related to Oxidation-Reduction Processes*

Many genes involved in oxidation-reduction processes were identified as DEGs (Figure 6, Table S8), indicating that the cellular redox balance was disturbed by exposure to the pollutant mixtures, consistent with the ROS measurements. Among the differentially expressed oxidation-reduction-related genes, some antioxidant genes exhibited increased expression. The most upregulated genes included a thioredoxin-like gene with log2 fold changes of 3.73 and 3.38 upregulated expression after 48 and 72 h, respectively. Glutathione *S*-transferase (*PHATRDRAFT\_37658*, *GST*) was also upregulated due to exposure to the mixtures, with upregulation by 1.47 and 2.59 log2 fold changes after 48 and 72 h exposure, respectively.

**Figure 6.** Heatmap of differentially expressed genes involved in oxidation-reduction processes that responded to exposure to mixtures of BDE-47 and nickel. Only genes with |log2 fold| changes > 2 and *p* < 0.05 after 48 h and/or 72 h are shown.
