Integrated Multi-Omics Analysis Reveals Molecular Signatures Associated with Growth Divergence in Mandarin Fish (Siniperca chuatsi).
4 affiliations
- 1National Engineering Research Center for Freshwaters (Beijing), Beijing Key Laboratory of Fisheries Biotechnology, Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100068, China.
- 2College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China.
- 3National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
- 4Department of Animal Science, Nnamdi Azikiwe University, Awka 420110, Anambra State, Nigeria.
Abstract
Within-cohort growth heterogeneity constrains aquaculture productivity, and its molecular correlates in carnivorous teleosts are poorly described. We compared the three heaviest and the three lightest individuals (n = 3 biological replicates per group, one fish per replicate) from a single cohort of mandarin fish (Siniperca chuatsi) at 90 days post-hatch, which differed 3.09-fold in body mass (p = 7.1 × 10⁻⁵), by combining muscle RNA sequencing with label-free quantitative proteomics of muscle and liver. Muscle transcriptomics identified 827 differentially expressed genes. The proteasome (ko03050) was the only KEGG pathway reaching significance, with all 14 contributing subunits being more abundant in slow-growing fish, and GO enrichment recovered proteasome, peptidase and endopeptidase complexes alongside serine-type peptidase activities in the same direction. Proteomics identified 37 differentially abundant proteins in muscle and 24 in liver at a nominal threshold. Protein-level gene set enrichment analysis showed negative enrichment of oxidative phosphorylation (NES = -1.96, adjusted p = 0.001) and of mitochondrial proteins (NES = -1.77, adjusted p = 0.005) in fast-growing muscle. Haemoglobin subunits were more abundant in fast-growing muscle and liver at the protein level, while muscle haemoglobin transcripts showed paralog-specific differences. The cross-sectional extreme-phenotype design identifies molecular signatures associated with the observed growth phenotype without establishing causality. The dataset provides candidate genes and proteins for functional study in S. chuatsi.
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BibTeX
@article{ahamba2026integrated,
title = {{Integrated Multi-Omics Analysis Reveals Molecular Signatures Associated with Growth Divergence in Mandarin Fish (Siniperca chuatsi).}},
author = {Ifeanyi Solomon Ahamba and Lionel Kinkpe and Xin Zhang and Xiaoli Yao and Christian Uchechukwu Ekugba and Hongxia Hu and Ran Cui},
journal = {International journal of molecular sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27198578},
url = {https://europepmc.org/article/MED/42883830},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrated Multi-Omics Analysis Reveals Molecular Signatures Associated with Growth Divergence in Mandarin Fish (Siniperca chuatsi).
AU - Ifeanyi Solomon Ahamba
AU - Lionel Kinkpe
AU - Xin Zhang
AU - Xiaoli Yao
AU - Christian Uchechukwu Ekugba
AU - Hongxia Hu
AU - Ran Cui
PY - 2026
DA - 2026/09/25
JO - International journal of molecular sciences
DO - 10.3390/ijms27198578
UR - https://europepmc.org/article/MED/42883830
AB - Within-cohort growth heterogeneity constrains aquaculture productivity, and its molecular correlates in carnivorous teleosts are poorly described. We compared the three heaviest and the three lightest individuals (n = 3 biological replicates per group, one fish per replicate) from a single cohort of mandarin fish (Siniperca chuatsi) at 90 days post-hatch, which differed 3.09-fold in body mass (p = 7.1 × 10⁻⁵), by combining muscle RNA sequencing with label-free quantitative proteomics of muscle and liver. Muscle transcriptomics identified 827 differentially expressed genes. The proteasome (ko03050) was the only KEGG pathway reaching significance, with all 14 contributing subunits being more abundant in slow-growing fish, and GO enrichment recovered proteasome, peptidase and endopeptidase complexes alongside serine-type peptidase activities in the same direction. Proteomics identified 37 differentially abundant proteins in muscle and 24 in liver at a nominal threshold. Protein-level gene set enrichment analysis showed negative enrichment of oxidative phosphorylation (NES = -1.96, adjusted p = 0.001) and of mitochondrial proteins (NES = -1.77, adjusted p = 0.005) in fast-growing muscle. Haemoglobin subunits were more abundant in fast-growing muscle and liver at the protein level, while muscle haemoglobin transcripts showed paralog-specific differences. The cross-sectional extreme-phenotype design identifies molecular signatures associated with the observed growth phenotype without establishing causality. The dataset provides candidate genes and proteins for functional study in S. chuatsi.
SN - 1422-0067
ER -