3.5. Differentially expressed genes in brain and thoracic ganglion between sexes based on Illumina sequencing results
Illumina sequencing was performed on brain and thoracic ganglion tissues of the female and male prawns, separately. After processing the raw reads, clean reads were obtained. The percentage of valid bases in all reads exceeded 92%, and the Q30 value of all sequences per library was as high as 94% (Table S5). Using the annotated unigenes as reference sequences, Illumina sequences were mapped to the reference sequences, and the mapped rates were 83.92% (male thoracic ganglion) to 90.49% (male brain) for all Illumina sequences in each library (far exceeding the standard of 70% non-pollution conditions). Further, 79.06%-85.76% of the Illumina sequences were matched in proper pairs (Table S6).
Volcano plots showed that the sex-based gene expression levels were distinguishable and statistically significant (p value < 0.05 and absolute value of log2-fold change > 2) (Figure 7). Compared with female prawns, male prawn brain and thoracic ganglia displayed 2,416 and 3,280 upregulated differentially expressed genes (DEGs), 2,871 and 2,931 DEGs were down-regulated, and 3,575 and 4,499 DEGs were exclusively expressed. 1,712 DEGs were shared by male and female prawns. GO annotation of DEGs revealed the top up-regulated genes in biological process, cellular component, molecular function categories in proper sequence to be hemolymph coagulation, extracellular region, lipid transporter activity for brain (Figure S4), as well as cell surface pattern recognition receptor signaling pathway, 4-aminobutyrate transaminase complex and its activity for thoracic ganglion (Figure S5). Growth-related genes in GO molecular function were actin binding (GO: 0003779), transforming growth factor beta receptor activity (GO: 0005026) etc. (Table 2). KEGG pathway annotation showed that DEGs were sorted into translation, transcript, protein folding, sorting, and degradation for the brain (Figure S6) and thoracic ganglion (Figure S7).