# Transcriptomic Analysis of Trachinotus ovatus Under Flow Velocity Stress

## TL;DR

This study explores how Trachinotus ovatus fish respond to different water flow speeds at the molecular level, revealing key biological processes affected by stress and suggesting optimal conditions for deep-sea aquaculture.

## Contribution

The study identifies a critical flow velocity threshold and molecular mechanisms of adaptation in T. ovatus under flow stress, offering practical guidance for deep-sea aquaculture.

## Key findings

- High flow velocity (90 cm/s) acts as a critical threshold for inducing physiological stress responses in T. ovatus.
- Glycolysis-related genes are upregulated under moderate to high flow, while lipid metabolism genes are downregulated.
- Activation of the unfolded protein response (UPR) and reduced anti-apoptotic gene expression suggest stress limits at 90 cm/s.

## Abstract

Water flow is an important environmental factor affecting fish physiology. In this study, we performed liver transcriptome sequencing of Trachinotus ovatus to explore their molecular responses under different flow velocity stresses. The results revealed that moderate to high flow velocities significantly affected key biological processes, including energy metabolism, protein homeostasis, and endoplasmic reticulum stress. Notably, a high flow velocity of 90 cm/s appeared to serve as a critical threshold inducing these physiological responses. In practical applications, deep and open-sea aquaculture often faces challenges such as strong currents and complex hydrodynamic conditions. Therefore, our findings provide new insights into the molecular adaptation mechanisms of T. ovatus under flow velocity stress, and offer a valuable reference for the site selection of deep-sea cage aquaculture systems.

Trachinotus ovatus is a euryhaline, warm-water pelagic fish species with strong adaptability, rapid growth, and a high survival rate, making it one of the most important marine aquaculture species in China. In recent years, extensive experience has been accumulated in the cage farming of T. ovatus, but whether it can adapt to deep-sea environments and grow normally remains a current research focus. This study used RNA-Seq sequencing technology to analyze the gene expression changes in the liver of T. ovatus under three conditions: rest (0 cm/s), medium flow velocity (54 cm/s), and high flow velocity (90 cm/s). Through differential expression analysis, Short Time-series Expression Miner (STEM) analysis and protein–protein interaction (PPI) network analysis, a total of 5107 differentially expressed genes (DEGs), three significantly expressed gene profiles (profile6, profile1, and profile5), and 15 hub genes were identified. The results showed that changes in flow speed significantly impacted key biological processes such as energy metabolism, protein homeostasis, and endoplasmic reticulum (ER) stress response. Under moderate and high flow conditions, glycolysis-related genes were upregulated to meet the energy demands of swimming, while the downregulation of the PPARγ-RXRG complex and its downstream genes in the lipid metabolism pathway suggested a limitation in its fatty acid β-oxidation capacity. At the same time, protein synthesis was enhanced, and the unfolded protein response (UPR) was activated to help cope with ER stress. Furthermore, when the flow speed reached 90 cm/s, the expression of UPR- related genes and the anti-apoptotic factor JNK significantly decreased, suggesting that the stress response was nearing its limit and could potentially trigger cell apoptosis. These findings provide new insights into the molecular adaptation mechanisms of T. ovatus to flow speed stress and offer theoretical support for its rational farming in deep-sea cages, suggesting that the water flow speed in farming should not exceed 90 cm/s.