Comparative transcriptome sequencing and weighted coexpression network analysis reveal growth-related hub genes and key pathways in the Chinese soft-shelled turtle (Pelodiscus sinensis)

The Chinese soft-shelled turtle (Pelodiscus sinensis) exhibits sexual dimorphism. Compared with females, males are considered to have higher economic value due to their accelerated growth, greater body mass, and longer skirt width. Studies focused on these sex disparities have largely neglected potential sex differences in growth. Here, we performed RNA sequencing of muscle tissue components from 1-year-old specimens to reveal gene expression patterns in P. sinensis. In our male and female cohorts, our analysis revealed, respectively, 388 and 526 upregulated differentially expressed genes (DEGs) and 1129 and 635 downregulated DEGs. Through weighted coexpression network analysis (WGCNA) and integration with phenotype data, we established two main gene modules: a light yellow module encompassing 191 genes (e.g., ACACB, CTH, HADHA, and CTNNB) that demonstrated a positive correlation with population traits, and a black module comprising 298 genes (e.g., CAV3, PIK3CD, SMAD3, and VEGFA) that demonstrated a negative correlation with population traits. We also performed a DEG evaluation and gene set enrichment analysis across individuals of different sizes and noted that pathways such as protein digestion and assimilation (ko04974), were substantially augmented in larger specimens. In these pathways, the collagen (COL) and solute carrier (SLC) gene families were noted to be crucial for sustaining body structure and facilitating nutrient and metabolite transportation. In conclusion, we elucidated the essential modules, pivotal genes, and pathways involved in gene expression differences among various P. sinensis size groupings. Our results provide novel insights for future studies on growth discrepancies in P. sinensis.