## 2 Results
### Identification and Enrichment Analysis of DEGs and DEPs  
As the treatment time increased from day 0 to day 7, the numbers of DEGs increased dramatically in the samples of _H. pluvialis_. The number of DEGs in the pairwise comparison of B257 vs. B07 was significantly higher than that of B252 vs. B02, suggesting that SA showed a weak effect on the microalgae in the early stage under the blue light culture and an enhanced effect in the late stage of the blue light treatment (Figure 1A). The most and the least numbers of DEGs of 29,295 and 76 were revealed in the pairwise comparisons of B07 vs. N and B252 vs. B02, respectively. As the treatment time of blue light irradiation increased, both the numbers of up-regulated and down-regulated genes increased significantly. In the groups treated with SA, there were only 76 DEGs, compared with the blue light group on day 2 of the treatment with blue light irradiation. However, on day 7 of the treatment with blue light irradiation, the numbers of up-regulated and down-regulated genes of the groups added with SA increased to 2187 and 9496, respectively (Figure 1A). The most and the least numbers of DEPs of 1385 and 52 were revealed in the pairwise comparisons of B07 vs. N and B257 vs. B07, respectively (Figure 1B).  
Figure 1: Differentially expressed genes (**A**) and proteins (**B**) identified among different pairwise comparisons of _Haematococcus pluvialis_.  
To further investigate the effects of blue light and SA on _H. pluvialis_, we selected unigenes with significant changes in transcripts and proteins to perform the enrichment analyses based on both GO (Figure S3) and KEGG (Figure S4) databases (Table S3).  
The results of the GO enrichment analysis showed that, on the second day of the treatment with blue light irradiation, most of the unigenes were annotated to carbon metabolism, e.g., glycolytic process, gluconeogenesis, and tricarboxylic acid cycle (Figure S3A). Notably, most genes, in response to cadmium ion, showed significant changes in their expressions. The results of the KEGG enrichment analysis showed that on the second day of the treatment with blue light irradiation, most of the unigenes were mainly enriched in metabolic pathways of energy metabolism, e.g., carbohydrate metabolism, metabolism of terpenoids and polyketides, and lipid metabolism (Figure S4A). On day 7 of the treatment with blue light irradiation, the unigenes showing significant changes in expression were mainly annotated to the GO terms related to proteins, e.g., translation, protein renaturation, and protein ubiquitin (Figure S3B), while the results of KEGG enrichment showed that the proportion of metabolic pathways of protein folding, sorting, and degradation was increased (Figure S4B). On the day 2 of the treatment with SA, no significantly expressed transcripts and proteins were observed. On day 7, with the addition of SA, most unigenes were annotated to GO terms of regulation of metabolic process, such as reactive oxygen species metabolic process, regulation of RNA metabolic process, and positive regulation by organization of apoptotic process (Figure S3C), while the results of KEGG enrichment analysis revealed that the significantly enriched metabolic pathways were related to infectious diseases (Figure S4C). These results were consistent with those reported previously, showing that SA, as one of the important signal molecules, played a vital role in disease resistance in plants [24].