Integrated Histological and Transcriptomic Analyses Reveal Distinct Structural and Molecular Features of the Calipash and Muscle in the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)

Calipash and muscle are the two most economically important edible tissues in Chinese soft-shelled turtle (Pelodiscus sinensis), However, the molecular and structural basis underlying their tissue-specific characteristics remains insufficiently understood. In this study, histological and protein-level analyses revealed that the calipash exhibits a highly organized multilayered architecture, in contrast to the myofiber-dominated organization of muscle. Type I collagen was highly abundant throughout the calipash and showed a spatially heterogeneous distribution, with particularly dense deposition in the outer layers and a mixture of type I and type III collagens in the innermost stromal layer. In contrast, collagen in the muscle was mainly restricted to the interstitial spaces and was predominantly composed of type I collagen, with relatively limited type III collagen. Using calipash as the reference group, transcriptome sequencing identified 6916 differentially expressed genes (DEGs) between calipash and muscle, including 3453 genes upregulated and 3463 genes downregulated in calipash. Calipash-specific genes were predominantly enriched in epidermal development, keratinocyte differentiation, ECM organization, and immune-related pathways, consistent with its specialized skin-like architecture and collagen-rich ECM. In contrast, muscle-specific genes were mainly associated with oxidative phosphorylation, mitochondrial function, myofibril assembly, and muscle contraction, in line with its mitochondria-enriched contractile architecture and energy-demanding characteristics. Focusing on collagen gene families, we found that col1a1/2 exhibited the highest transcriptional abundance in both tissues. Notably, qPCR and WB confirmed that this transcriptional advantage translated into substantial type I collagen protein deposition. These findings provide new insights into the molecular basis of tissue-specific texture and the biological differences between calipash and muscle in P. sinensis.