Abstract
The Turpan minnow (Phoxinus grumi) is a small endemic fish species inhabiting the extreme environment of the Turpan Basin in Xinjiang, China, holding significant value for evolutionary and conservation biology research. However, the absence of a high-quality reference genome has severely constrained studies on its adaptive evolution and conservation genetics, in stark contrast to the available chromosome-level genomes of its congeners, such as Phoxinus phoxinus. A total of 240.38 Gb of sequencing data was generated in this study, comprising 44.12Gb (53.35×) of PacBio HiFi reads, 50.36 Gb (60.90×) of Illumina reads, 120.59 Gb (133.95×) of Hi-C data and 25.31 Gb of RNA sequencing data, which enabled the successful assembly of a chromosome-level genome for P. grumi. The assembled genome has a total size of 900.41 Mb, with 97.58% of the sequences anchored onto 25 chromosomes. The contig N50 and scaffold N50 reached 17.52 Mb and 34.99 Mb, respectively. BUSCO assessment indicated a genome completeness of 98.1%. We predicted a total of 24,224 protein-coding genes, of which 90.8% were functionally annotated. This high-quality reference genome will serve as a key genetic resource for in-depth exploration of the environmental adaptation mechanisms and species conservation of P. grumi.
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Data availability
The raw sequencing data are available in the NCBI databases under Bioproject accession number PRJNA1399684. Additionally, the assembled genome has been deposited in GenBank. Furthermore, all datasets are available under the BioProject accession number PRJCA050662 in the Genome Warehouse (GWH) at the National Genomics Data Center (NGDC). The data are publicly accessible via the following link at https://ngdc.cncb.ac.cn/gwh. Raw reads have been deposited in NGDC (Hi-C: SAMC6098139; Illumina: SAMC6098138; PacBio HiFi: SAMC6098137). The final genome assembled and annotation files have been deposited in Figshare platform via https://doi.org/10.6084/m9.figshare.30572321.v1.
Code availability
No custom code or scripts were utilized in this study, all commands and pipelines involved in data processing were executed in accordance with the manuals and protocols provided by the bioinformatic software employed. The specific versions of software packages and corresponding parameters implemented for each analytical step are explicitly detailed in the Methods section to ensure reproducibility.
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Acknowledgements
This research was supported by the Third Xinjiang Scientific Expedition Program (No. 2022xjkk1505), the Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms (No. KFKT2402), the China Postdoctoral Science Foundation (No. 339494), and the Xinjiang Uygur Autonomous Region Tianchi Talent Introduction Program.
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J.W. and H.C. conducted the bioinformatic analyses including genome assembly and gene annotation, and drafted the manuscript. P.Y. processed and refined the images and contributed to data analysis. W.G., X.W., X.L., Y.H. and M.G. collected the samples and performed the animal experiments. J.W. and W.G. revised and edited the manuscript. All authors read and approved the final manuscript.
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Wang, J., Chang, H., Yang, P. et al. A chromosomal-level genome assembly of Phoxinus grumi (Cypriniformes: Leuciscidae). Sci Data (2026). https://doi.org/10.1038/s41597-026-07087-5
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DOI: https://doi.org/10.1038/s41597-026-07087-5
