Comparative Transcriptome Profiling Reveals Developmental Regulatory Networks in Rainbow Trout Eggs and Hatched Larvae.
- 1Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China.
- 2Jiangsu (Marine) Salmon and Trout Science and Technology Innovation Center, Yellow Sea Laboratory for Blue Seed Industry, Yancheng 224000, China.
- 3College of Marine and Biology Engineering, Yancheng Institute of Technology, No. 1, Middle Xiwang Avenue, Yancheng 224000, China.
Abstract
Rainbow trout (Oncorhynchus mykiss) is a globally important cold-water aquaculture species, yet the molecular events underlying the transition from embryo to free-living larva remain poorly resolved. In this study, eukaryotic reference-based transcriptome sequencing was used to compare genome-wide gene expression profiles between eggs (eyed-egg stage) and newly hatched larvae of O. mykiss. A total of 618 differentially expressed genes (DEGs) were identified, of which 297 were upregulated and 321 downregulated. Gene Ontology (GO) enrichment analysis showed that DEGs were significantly enriched in immune system process, response to stimulus, and biological regulation. Within the immune system process category, 4 DEGs were upregulated and 11 were downregulated in larvae, indicating a more complex remodelling of immune-related gene expression than simple activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified only Glycolysis/Gluconeogenesis (map00010) as significantly enriched (padj < 0.05). Nitrogen metabolism (map00910) and tryptophan metabolism (map00380) showed enrichment trends but were not statistically significant after multiple-testing correction. Because these pathways contained only a small number of DEGs and displayed mixed regulation, no overall pathway-level up- or down-regulation was inferred. These results suggest a possible metabolic remodelling during the transition from yolk-dependent anabolism to catabolic utilization in larvae. Transcript assembly further identified 134,770 potential novel isoforms and 2902 intergenic transcripts classified as putative novel transcripts, enriching the genome annotation of O. mykiss. Trend clustering indicated coordinated regulation of immune and stress-response genes together with downregulation of amino acid and energy metabolism genes, revealing programmed temporal regulation during this developmental transition. These findings provide foundational data for understanding early development in rainbow trout and candidate molecular targets for health-oriented aquaculture management.
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BibTeX
@article{sui2026comparative,
title = {{Comparative Transcriptome Profiling Reveals Developmental Regulatory Networks in Rainbow Trout Eggs and Hatched Larvae.}},
author = {Yanming Sui and Mijun Xu and Jingtao Liu and Yiyun Zhang and Yuanhao Ren and Bo Qin and Na Ying and Tingting Lin and Siping Li and Hanfeng Zheng and Lei Li},
journal = {Biology},
year = {2026},
month = oct,
doi = {10.3390/biology15201872},
url = {https://europepmc.org/article/MED/42939473},
note = {CC BY},
}
RIS
TY - JOUR
TI - Comparative Transcriptome Profiling Reveals Developmental Regulatory Networks in Rainbow Trout Eggs and Hatched Larvae.
AU - Yanming Sui
AU - Mijun Xu
AU - Jingtao Liu
AU - Yiyun Zhang
AU - Yuanhao Ren
AU - Bo Qin
AU - Na Ying
AU - Tingting Lin
AU - Siping Li
AU - Hanfeng Zheng
AU - Lei Li
PY - 2026
DA - 2026/10/16
JO - Biology
DO - 10.3390/biology15201872
UR - https://europepmc.org/article/MED/42939473
AB - Rainbow trout (Oncorhynchus mykiss) is a globally important cold-water aquaculture species, yet the molecular events underlying the transition from embryo to free-living larva remain poorly resolved. In this study, eukaryotic reference-based transcriptome sequencing was used to compare genome-wide gene expression profiles between eggs (eyed-egg stage) and newly hatched larvae of O. mykiss. A total of 618 differentially expressed genes (DEGs) were identified, of which 297 were upregulated and 321 downregulated. Gene Ontology (GO) enrichment analysis showed that DEGs were significantly enriched in immune system process, response to stimulus, and biological regulation. Within the immune system process category, 4 DEGs were upregulated and 11 were downregulated in larvae, indicating a more complex remodelling of immune-related gene expression than simple activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified only Glycolysis/Gluconeogenesis (map00010) as significantly enriched (padj < 0.05). Nitrogen metabolism (map00910) and tryptophan metabolism (map00380) showed enrichment trends but were not statistically significant after multiple-testing correction. Because these pathways contained only a small number of DEGs and displayed mixed regulation, no overall pathway-level up- or down-regulation was inferred. These results suggest a possible metabolic remodelling during the transition from yolk-dependent anabolism to catabolic utilization in larvae. Transcript assembly further identified 134,770 potential novel isoforms and 2902 intergenic transcripts classified as putative novel transcripts, enriching the genome annotation of O. mykiss. Trend clustering indicated coordinated regulation of immune and stress-response genes together with downregulation of amino acid and energy metabolism genes, revealing programmed temporal regulation during this developmental transition. These findings provide foundational data for understanding early development in rainbow trout and candidate molecular targets for health-oriented aquaculture management.
SN - 2079-7737
ER -