Transcriptomic Responses of the Endangered Endemic Fish Aspiorhynchus laticeps to Salinity–Alkalinity and Water Flow Stress
TL;DR
A combination of ecological experiments and transcriptome sequencing technology was used to study the differences in gene expression patterns among individuals under different salinities and flow conditions, and revealed that TNF signal transduction, the NF-κB pathway, and metabolic regulation were significantly enriched among the DEGs.
Abstract
Simple Summary To elucidate the poorly understood adaptive mechanisms of Aspiorhynchus laticeps, a critically endangered fish endemic to Xinjiang’s Tarim Basin, under extreme aquatic stress, this study aimed to unravel the evolutionary adaptation patterns of plateau freshwater fish to environmental pressures. By integrating ecological experiments with transcriptome sequencing, we exposed A. laticeps to varied salinity–alkalinity and flow regimes for comparative analysis. We identified 1847 differentially expressed genes that were significantly enriched in TNF/NF-κB immune signaling and metabolic pathways. Experimental evidence confirmed that high saline–alkali stress activates these pathways and modulates target genes to enhance stress tolerance, whereas flow fluctuations regulate energy metabolism through distinct functional genes. This research provides molecular insights for artificial habitat regulation and population conservation of A. laticeps in the Tarim River, and offers a scientific foundation for endangered fish protection, germplasm improvement, and ecological rehabilitation in arid alpine zones. Abstract To understand the adaptive evolution of endangered plateau freshwater fishes to environmental stress and to better explore the underlying mechanisms in Aspiorhynchus laticeps—a critically endangered fish endemic to the Tarim Basin, Xinjiang, China—a combination of ecological experiments and transcriptome sequencing (RNA-seq) technology was used to study the differences in gene expression patterns among individuals under different salinities and flow conditions. This experiment included four treatment groups (CON, H-SA-S, L-SA, L-SA-S). A. laticeps specimens with an average weight of 2.92 ± 0.62 g and a body length of 58.22 ± 5.10 mm were selected, with three biological replicates for a 96 h combined stress treatment. Moreover, the relationships between these differences and the aquatic environment were analyzed. A total of 1847 differentially expressed genes (DEGs), including 935 upregulated genes and 912 downregulated genes, were identified under different aquatic environment stress modes. GO and KEGG enrichment analyses revealed that TNF signal transduction, the NF-κB pathway, and metabolic regulation were significantly enriched among the DEGs (p < 0.05). High salinity–alkali stress significantly activates the TNF/NF-κB pathway, regulates MST1, LOC107702867, LOC113110979 and other genes to enhance the body’s resistance; water flow changes mainly regulate energy metabolism through genes such as NEHOM01_1600 and gptl. These findings provide an important scientific basis for the ecological adaptability, protection, and proliferation of endemic and endangered fish in China, as well as for germplasm innovation to address ecological deterioration in plateau fishes in alpine and arid areas. This study provides a molecular-level theoretical foundation for artificial habitat regulation and the conservation of endangered Aspiorhynchus laticeps populations in the Tarim River.