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, SRP583726[28](https://www.nature.com/articles/s41597-025-06478-4#ref-CR28 “NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:S…
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.
References
Liang, H. W., Guo, S. S., Li, Z., Luo, X. Z. & Zou, G. W. Assessment of genetic diversity and population structure of swamp eel in China. Biochem Syst Ecol 68, 81–87, https://doi.org/10.1016/j.bse.2016.06.006 (2016).
Yang, D. A. C., Fang and Ruan, Guoliang. Aquaculture of the paddy eel, Monopterus albus. Aquaculture in China: Success stories and modern trends (2018). 1.
Zhao, X. Y. et al. Chromosome-scale assembly of the Monopterus genome. Gigascience 7, https://doi.org/10.1093/gigascience/giy046 (2018). 1.
Jiang, Y. A. L., Hongrui and Hou, Mingxi and Chen, Ji and Tao, Binbin and Zhu, Zuoyan and Song, Yanlong and Hu, Wei. Aromatase inhibitor induces sex reversal in the protogynous hermaphroditic rice field eel (Monopterus albus). Aquaculture (2022). 1.
Chen, H. J. et al. Blood cell identification and hematological analysis during natural sex reversal in rice field eel (Monopterus albus). Aquaculture 538, https://doi.org/10.1016/j.aquaculture.2021.736543 (2021). 1.
Cheng, H., He, Y. & Zhou, R. Swamp eel (Monopterus albus). Trends Genet 37, 1137–1138, https://doi.org/10.1016/j.tig.2021.09.007 (2021).
Cheng, H., Guo, Y., Yu, Q. & Zhou, R. The rice field eel as a model system for vertebrate sexual development. Cytogenet Genome Res 101, 274–277, https://doi.org/10.1159/000074348 (2003).
Li, Y. Y. et al. ASER: Animal Sex Reversal Database. Genom Proteom Bioinf 19, 873–881, https://doi.org/10.1016/j.gpb.2021.10.001 (2021).
Cheng, H. & Zhou, R. Decoding genome recombination and sex reversal. Trends Endocrinol Metab 33, 175–185, https://doi.org/10.1016/j.tem.2021.12.002 (2022).
Cheng, Y. B. et al. Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome. Cell and Bioscience 10, https://doi.org/10.1186/s13578-020-00432-0 (2020). 1.
Wang, X. et al. Cellular fate of intersex differentiation. Cell Death Dis 12, 388, https://doi.org/10.1038/s41419-021-03676-x (2021).
Nozu, R., Kadota, M., Nakamura, M., Kuraku, S. & Bono, H. Meta-analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes. Genes Cells 29, 1052–1068, https://doi.org/10.1111/gtc.13166 (2024).
Torre, D. et al. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 14, 6902, https://doi.org/10.1038/s41467-023-42558-y (2023).
Liao, X. et al. Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data. Sci Data 10, 105, https://doi.org/10.1038/s41597-023-02014-4 (2023).
Wang, K. et al. Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nat Commun 10, 4714, https://doi.org/10.1038/s41467-019-12575-x (2019).
Klemm, S. L., Shipony, Z. & Greenleaf, W. J. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet 20, 207–220, https://doi.org/10.1038/s41576-018-0089-8 (2019).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21, https://doi.org/10.1093/bioinformatics/bts635 (2013).
Liao, Y., Smyth, G. K. & Shi, W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41, e108, https://doi.org/10.1093/nar/gkt214 (2013).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq 2. Genome Biol 15, 550, https://doi.org/10.1186/s13059-014-0550-8 (2014).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100, https://doi.org/10.1093/bioinformatics/bty191 (2018).
Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650–1667, https://doi.org/10.1038/nprot.2016.095 (2016).
Niknafs, Y. S., Pandian, B., Iyer, H. K., Chinnaiyan, A. M. & Iyer, M. K. TACO produces robust multisample transcriptome assemblies from RNA-seq. Nat Methods 14, 68–70, https://doi.org/10.1038/nmeth.4078 (2017).
Kuo, R. I. et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. Bmc Genomics 21, 751, https://doi.org/10.1186/s12864-020-07123-7 (2020).
Zhao, X. Y. et al. GenBank https://identifiers.org/insdc.gca:GCA_001952655.1 (2017). 1.
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137, https://doi.org/10.1186/gb-2008-9-9-r137 (2008).
Ross-Innes, C. S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389–U177, https://doi.org/10.1038/nature10730 (2012).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP578156 (2025). 1.
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP583726 (2025). 1.
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP584005 (2025). 1.
Zhao, Y. GEO. https://identifiers.org/geo/GSE312266 (2025). 1.
Li, Y. Y. GenBank https://www.ncbi.nlm.nih.gov/nuccore/GLKV00000000.1 (2025). 1.
Li, Y. Y. The NCBI and GASR isoforms and putative gene-CREs linkages during sex reversal for M. albus. Zenodo https://doi.org/10.5281/zenodo.17470351 (2025).
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.
Author information
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
- Yangyang Li
- Yuanli Zhao
- Hongrui Luo
- Kaifeng Meng
- Jiarui Song
- Jiayi Yang
- Wei Hu
- 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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Competing interests
The authors declare no competing interests.
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Cite this article
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
Received: 25 July 2025
Accepted: 15 December 2025
Published: 27 December 2025
DOI: https://doi.org/10.1038/s41597-025-06478-4