Data availability

All datasets generated and analyzed during this study have been deposited in publicly accessible repositories. The RNA-seq, Iso-Seq, and ATAC-seq datasets are organized under the GEO SuperSeries GSE31226630, and the corresponding raw reads are available in the NCBI Sequence Read Archive (SRA) under the BioProject accession numbers SRP57815627, SRP58372628, and SRP58400529, respectively. The transcriptome assembly generated in this study has been deposited in the NCBI TSA database under accession number GLKV00000000.131. All related data, including the NCBI and GASR isoforms and Table S1 containing putative gene–CRE linkages during sex reversal, are publicly available via Zenodo (https://doi.org/10.5281/zenodo.1747035132).

Code availability

All software employed throughout this research is openly accessible, with parameters explicitly outlined within the Methods section. When specific settings were not detailed for any given tool, recommended defaults from the original developers were applied. The code for this paper was deposited at GitHub: https://github.com/liyangyang12/Multi-omics-data-of-Monopterus-albus.

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Acknowledgements

This work was supported by grants from the from the National Natural Science Foundation of China (32425055), Natural Science Foundation of Hubei Province (2023BBB172), Fund Projects Supporting High-quality Seed Industry Development of Hubei Province (HBZY2023B009) and Foundation of Hubei Hongshan Laboratory (2022hszd022) to D Luo. China Postdoctoral Science Foundation (2025M773127) to Y Li.

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Author notes

These authors contributed equally: Yangyang Li, Yuanli Zhao.

Authors and Affiliations

Department of Obstetrics and Gynecology, Center for Reproductive Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, 32200, China

Yangyang Li 1.

Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China

Yuanli Zhao, Hongrui Luo, Kaifeng Meng, Jiarui Song, Wei Hu & Daji Luo 1.

College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China

Kaifeng Meng & Daji Luo 1.

College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China

Jiarui Song & Daji Luo 1.

State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China

Jiayi Yang

Authors

1. Yangyang Li
2. Yuanli Zhao
3. Hongrui Luo
4. Kaifeng Meng
5. Jiarui Song
6. Jiayi Yang
7. Wei Hu
8. Daji Luo

Contributions

Yangyang Li: Investigation, Data curation, Visualization, Software, Resources, Writing original draft and review & editing. Yuanli Zhao: Data curation, Visualization, Software, Writing-review & editing. Hongrui Luo: Sampling. Kaifeng Meng: Data curation, Visualization. Jiarui Song: Validation. Jiayi Yang: Validation. Wei Hu: Funding acquisition, Resources, Writing-review & editing. Daji Luo: Conceptualization, Funding acquisition, Methodology, Project administration, Resources, Supervision, Writing original draft and review & editing.

Corresponding authors

Correspondence to Wei Hu or Daji Luo.

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Li, Y., Zhao, Y., Luo, H. et al. Multi-omics integration identifies diverse transcripts and chromatin accessibility profiles in Monopterus albus gonads. Sci Data (2025). https://doi.org/10.1038/s41597-025-06478-4

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Received: 25 July 2025

Accepted: 15 December 2025

Published: 27 December 2025

DOI: https://doi.org/10.1038/s41597-025-06478-4