Comparative Transcriptome Sequencing Analysis Revealed Key Pathways and Hub Genes Related to Gill Raker Development in Silver Carp (Hypophthalmichthys molitrix)

The silver carp (<i>Hypophthalmichthys molitrix</i>) is a filter-feeding fish species, characterized by significant morphological transformations in its filter-feeding apparatus, particularly the gill rakers, which are closely associated with dietary changes throughout its development. Despite the importance of these morphological innovations, the molecular mechanisms driving these changes remain largely unexplored. To investigate this, we employed an integrative approach combining scanning electron microscopy (SEM) and comparative transcriptomics to examine the gill rakers at five critical developmental stages (6, 15, 30, 45, and 60 days post-hatching, dph). SEM analysis revealed a structural evolution from sparse, bump-like protrusions to a dense, interlocking mesh. Simultaneously, transcriptomic analysis identified 10,184 differentially expressed genes (DEGs), which showed significant enrichment in pathways such as Focal Adhesion, ECM-Receptor Interaction, and the PI3K-Akt Signaling Pathway. Gene Set Enrichment Analysis (GSEA) indicated a coordinated upregulation of collagen and integrin gene families during the early developmental transition (6 vs. 15 dph), highlighting their crucial role in the formation of the sieve structure. This study reveals the molecular mechanisms of gill raker development in silver carp, providing initial insights into genetic regulation of morphology for ecological adaptation. The findings connect developmental biology, evolutionary biology, and ecology.