The genus Sinocyclocheilus (golden-line fish) includes a dozen species of cave-dwelling blind fish and over thirty surface-dwelling sighted species. Cave environments are not only dark, but also generally nutrient poor. Cave-dwelling fish (cavefish) have convergently evolved a series of morphological adaptations to their eyes, pigmentation, brain, olfactory, and digestive systems. Although the brain expends a substantial fraction of an animal’s whole-body energy use, it is as yet unknown whether energy metabolism in the cavefish brain has adapted in food-limited cave environments.
We used RNA-seq to investigate the evolution of the cavefish (S. anophthalmus, eyeless golden-line) transcriptome by comparing gene expression to a surface-dwelling species (S. angustiporus, surface golden-line) from the same genus. Gene pathways related to cholesterol biosynthesis were significantly enriched in genes downregulated in cavefish. Two sterol regulatory element binding transcription factor genes, srebf1 and srebf2, and their down-stream genes, including genes encoding enzymes in cholesterol synthesis (hmgcs1, hmgcra, sqlea, fdft1, cyp51, lss, dhcr7, and idi1) were downregulated in the cavefish brain compared to surface fish brain.
Our comparative analyses provide molecular evidence for the regulation of cholesterol metabolism in the cavefish brain. Gene expression studies suggest that adaptations to dark, nutrient-poor cave environments in eyeless golden-line cavefish involved reduction in the rate of biosynthesis of cholesterol, thereby saving energy in adaptation to the cave environment.