Differential Expression and Alternative Splicing Pattern in Female and Male Groups Pelteobagrus ussuriensis with Different Growth Rate

TL;DR

This study explores how male and female Pelteobagrus ussuriensis fish regulate growth differently, focusing on gene expression and splicing in the liver and brain.

Contribution

The study reveals sex-specific differences in growth regulation through differential gene expression and alternative splicing in key organs.

Findings

Males showed growth regulation linked to lipid and cholesterol metabolism, while females involved broader metabolic processes.

Alternative splicing events were tissue-specific, with exon skipping in the liver and alternative first exon usage in the brain.

Transcript-level differences were identified that were not apparent at the gene level, emphasizing transcript diversity in growth regulation.

Abstract

Growth rate is an important factor that affects how efficiently farmed fish produce food; but, males and females may grow differently because they are regulated by different biological processes. In this study, we investigated why some male and female Pelteobagrus ussuriensis grow faster than others by comparing fast-growing and slow-growing individuals. We focused on two key organs, the liver and the brain, which play important roles in metabolism and growth control. We found that males and females use different biological pathways to regulate growth. In males, growth differences were mainly related to fat and cholesterol processing, while in females, growth differences involved a wider range of processes, including the use of sugars, fats, and proteins. Some genes directly related to growth and hormone regulation were also different between fast- and slow-growing fish. In the brain, growth-related differences were much smaller but still showed clear sex-specific patterns. We also discovered that fish produced different forms of the same gene, which influenced growth even when overall gene activity appears unchanged. These findings improve our understanding of how growth is regulated and may help develop better strategies for fish breeding and sustainable food production.

Growth rate is a key trait influencing productivity in aquaculture species, and its regulation often differs between males and females. In this study, Nanopore full-length RNA sequencing was used to investigate sex-specific growth regulation in the liver and brain of Pelteobagrus ussuriensis. Male and female groups each included three fast-growing and three slow-growing individuals. In liver tissue, 332 differentially expressed genes were identified in males and 266 in females. Male-biased genes were mainly involved in lipid and cholesterol metabolism, including the peroxisome proliferator-activated receptor signaling pathway, whereas females showed broader metabolic regulation involving carbohydrate, amino acid, and lipid metabolism, as well as growth-related genes such as IGFBP1, ESR1, and PGR. In brain tissue, fewer growth-associated differences were observed, with 26 differentially expressed genes in males and 45 in females. Alternative splicing analysis revealed strong tissue specificity, with approximately 2903 events in liver and 7412 in brain, dominated by exon skipping in liver and alternative first exon usage in brain. Isoform-level analysis further identified transcript differences not detected at the gene level, highlighting the importance of transcript diversity in growth regulation.

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