Brain Transcriptomics Reveals Molecular Mechanisms of Cave Adaptation in <i>Triplophysa</i> Loaches

Understanding the adaptive evolution of brain function in extreme environments remains a central challenge in evolutionary biology. This study investigates the molecular mechanisms underlying cave adaptation by comparing brain transcriptomes of sympatric cave-dwelling (<i>Triplophysa shilinensis</i>) and surface-dwelling (<i>Triplophysa xiangshuingensis</i>) loaches (<i>n</i> = 5 per ecotype). We generated a comprehensive dataset comprising 60.74 billion clean reads and identified 101,725 Unigenes. Bioinformatics analysis revealed significant differences in brain gene expression between the two ecotypes, with 27,194 differentially expressed genes (12,188 up-regulated and 15,006 down-regulated). In <i>T. shilinensis</i>, cave adaptation-associated genes were notably enriched in pathways related to insulin secretion and energy metabolism (<i>GLUT1</i>, <i>IRS1</i>, <i>PRKCA/PKCα</i>, <i>ACSL</i>), circadian rhythms and behavior (<i>CRY</i>, <i>FBXL3</i>, <i>CLOCK</i>, <i>NPY2R</i>), body coloration (<i>ADCY9</i>, <i>GNQA</i>), visual development (<i>RDH8</i>, <i>LRAT</i>, <i>CNGB1</i>), and olfactory sensation (<i>OLFR</i>, <i>ADCY3</i>, <i>PKA</i>, <i>CAMK2</i>). Strikingly, most differentially expressed genes were down-regulated in the cave-dwelling ecotype, a trend further validated by qRT-PCR. These expression patterns correlate with differential cave adaptation in <i>Triplophysa</i>, providing critical insights into the genetic basis of subterranean evolution. Our findings establish a foundational framework for future research on cave acclimatization mechanisms in this genus.