Abstract
Traccatichthys pulcher is an ornamental loach species recognized for its vibrant body coloration, characteristic black dorsal fin margin, and iridescent green lateral stripes. To advance genomic research on this species, a high-quality, near telomere-to-telomere (T2T) genome assembly was generated using PacBio HiFi, ONT ultra-long, and Hi-C sequencing technologies. The resulting haplotype-resolved assembly spanned approximately 623.68 Mb, with a contig N50 of 22.9 Mb, and was anchored onto 24 chromosomes. Telomeric sequences were detected at both ends of eight chromosomes and at one end of 13 chromosomes. Twenty-three chromosomes were entirely gapless, while a single gap was identified in the remaining chromosome. The assembly contained 119.1 Mb of repetitive elements, and 23 967 protein-coding genes were annotated. BUSCO analysis indicated high completeness, with 98.6% of conserved genes recovered. This high-quality, near T2T genome assembly offers a valuable and robust genetic resource for investigating molecular mechanisms, evolutionary processes, conservation biology, and selective breeding of T. pulcher.
Code availability
All computational tools used in this study are open-source and publicly available. Software versions and parameter settings are described in the Methods section. When unspecified, programs were executed using default settings according to the developers’ documentation.
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Acknowledgements
We would like to thank Yuan-Sheng Huang from Wuhan Benagen Technology Co., Ltd for his assistance in project management. We are grateful to Yu-Fan Liang from Sanya Boao Biotechnology Co., Ltd for his help in genome annotation. We greatly thank Jia-Jun Zhou from Zhejiang Forest Resource Monitoring Center for collecting, and Hao-Jun Chen for taking living photo of T. pulcher. We thank C. Watts for English corrections and suggestions. National Natural Science Foundation of China (NSFC32560121). Investigation of Fishery Resources and Habitat in the Pearl River Basin (ZJZX-10). Investigation and Monitoring Project of Biodiversity Backgroud Resources in Guilin Nature Reserve (GLZC2024-C3-990742-GXXL), Comprehensive Scientific Investigation Project of Guangxi Daguishan Crocodile Lizard National Nature Reserve, and Jilin Provincial Key R&D Project (20210202082NC).
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Li-Na Du and Zhuo-Cong Wang analyzed the data, prepared the manuscript, and providing funding acquisition. Zhuo-Ni Chen and Zhi-Xian Qin assembly and annotation of genome. Chen-Hong Li conceived and designed the study. All authors read and approved the final version of the manuscript.
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Du, LN., Wang, ZC., Chen, ZN. et al. Near telomere-to-telomere genome assembly of the stone loach (Traccatichthys pulcher). Sci Data (2026). https://doi.org/10.1038/s41597-026-06849-5
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DOI: https://doi.org/10.1038/s41597-026-06849-5
