Transcriptomic profiling reveals distinct nutrient-absorptive and immune-defensive zones in the Squalidus argentatus intestine

Abstract

The intestine serves as the primary site for nutrient digestion, absorption, and mucosal immunity in fish. However, the anatomical localization of these functions within the intestine of Squalidus argentatus , a commercially valuable cyprinid fish, remains poorly understood. In this study, we utilized high-throughput transcriptome sequencing to systematically analyze the functional regionalization across four distinct intestinal segments: the anterior intestine (AI), middle intestine (MI), anterior region of the posterior intestine (PI1), and posterior region of the posterior intestine (PI2). We generated 529,541,628 clean reads and assembled 127,441 unigenes. Differential expression and trend analyses revealed a potential gradient of physiological functions along the intestinal tract. The AI and MI were predominantly enriched in nutrient-absorptive pathways, including fat, vitamin, and protein digestion and absorption, indicating their primary role as major nutrient-absorptive zones. Conversely, the PI, particularly the PI2 segment, exhibited specific enrichment in immune defense pathways, including lysosomes, phagosomes, and cytokine receptor interactions. This segment showed abundant expression of key cathepsin genes ( ctsz , ctsh , ctsl , ctsb ), suggesting a specialized role in pathogen defense and antigen processing. Our findings reveal a distinct functional division in the S. argentatus intestine, where the anterior-mid regions (AI-MI) may specialize in nutrient processing, while the distal region (PI2) displays a transcriptional landscape indicative of a potential mucosal immune barrier. This study provides a crucial molecular foundation for understanding the digestive physiology of stomachless fish and offers practical insights for the development of segment-specific compound feeds to enhance growth and disease resistance in aquaculture.