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• Open access

• Published: 30 January 2026

• Zechen E ORCID: orcid.org/0009-0001-6857-47941,2,3,

• Fangyuan Xiong1,2,3,

• Yuansheng Zhu1,2,3,

• Li Wang1,2,3,

• Jiajun Zhang1,2,3,

• Shenghui Dong1,2,3 &

• …

• Mingxiang Lu1,2,3

Scientific Data , Article number: (2026) Cite this article

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Abstract

The longfin barb (Acrossocheilus longipinnis), a vulnerable cyprinid fish endemic to China’s Pearl River basin, is of significant conservation concern and also popular in the ornamental fish trade. To facilitate genetic research and molecular breeding for this species, we generated a high-quality genome by integrating PacBio HiFi long reads and Hi-C sequencing data. The final assembly spans approximately 936.04 Mb, achieving high continuity with a contig N50 of 36.09 Mb. Assessment of genome quality revealed excellent completeness (98.76% BUSCO score) and accuracy (QV = 54.46; GCI = 29.76; CRAQ = 96.40). The vast majority of the sequence (927.20 Mb, 99.06%) was successfully anchored to 25 chromosomes. Annotation predicted 24,718 protein-coding genes and identified approximately 553.06 Mb (59.09%) of repetitive elements. This high-quality chromosome-scale reference genome provides a crucial foundation for investigating the genomic underpinnings of A. longipinnis evolution and will significantly advance molecular breeding programs aimed at its conservation and sustainable utilization.

Data availability

Raw sequencing data have been deposited in the NCBI SRA database under BioProject accession number PRJNA1297891, with accession numbers as follows: PacBio HiFi: SRR3477099149; Hi-C: SRR3477099250; RNA sequencing: SRR3477099051; DNA short-read sequencing: SRR3477099352. The genome assembly has been uploaded to the GenBank database under the accession GCA_054083375.153. Moreover, the genome assembly, annotation files (GFF3, FASTA), and gene functional annotation datasets, are available via Figshare41. All datasets are publicly accessible without restrictions.

Code availability

No specific code or script was used in this work. Commands used for data processing were all executed according to the manuals and protocols of the corresponding software.

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Acknowledgements

This work is supported by Operating funds of Hongshui River Rare Fish conservation Center.

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Authors and Affiliations

Scientific Institute of Pearl River Water Resources Protection, Guangzhou, 510611, China

Zechen E, Fangyuan Xiong, Yuansheng Zhu, Li Wang, Jiajun Zhang, Shenghui Dong & Mingxiang Lu 1.

Hongshui River Rare Fish Conservation Center, Guigang, 537200, China

Zechen E, Fangyuan Xiong, Yuansheng Zhu, Li Wang, Jiajun Zhang, Shenghui Dong & Mingxiang Lu 1.

Engineering Research Center of Hongshui River Rare Fish Conservation, Guangxi Zhuang Autonomous Region, Guigang, 537200, China

Zechen E, Fangyuan Xiong, Yuansheng Zhu, Li Wang, Jiajun Zhang, Shenghui Dong & Mingxiang Lu

Authors

1. Zechen E
2. Fangyuan Xiong
3. Yuansheng Zhu
4. Li Wang
5. Jiajun Zhang
6. Shenghui Dong
7. Mingxiang Lu

Contributions

Zechen E conceived this study, designed the experiment, and performed data analysis. Fangyuan Xiong contributed to the experimental design, collected samples, and performed data analysis. Yuansheng Zhu and Li Wang provided funding and contributed to conceptualization. Jiajun Zhang and Shenghui Dong assisted in methodology and data curation. All authors have read and approved the final manuscript.

Corresponding author

Correspondence to Fangyuan Xiong.

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E, Z., Xiong, F., Zhu, Y. et al. Chromosome-level genome assembly of the longfin barb (Acrossocheilus longipinnis). Sci Data (2026). https://doi.org/10.1038/s41597-026-06656-y

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Received: 17 September 2025

Accepted: 19 January 2026

Published: 30 January 2026

DOI: https://doi.org/10.1038/s41597-026-06656-y