Abstract
Yaoshania pachychilus (Gastromyzontidae, Cypriniformes) is a benthic species inhabiting torrential mountain streams, where it attaches to rocks using adhesive pelvic and pectoral fins. Its juvenile black-white coloration has made it popular in the ornamental fish trade, yet wild populations face increasing threats. Here, we present the first chromosome-level genome assembly for this species, generated using PacBio HiFi and Hi-C technologies. The final assembly spans 451.24 Mb, with a contig N50 of 9.87 Mb, and 99.2% of the sequences are anchored onto 25 pseudo-chromosomes. We annotated repetitive elements accounting for 27.8% of the genome and predicted 21,816 protein-coding genes. BUSCO completeness exceeded 97% for both the genome assembly and gene annotation. This reference genome provides a valuable resource for investigating torrent adaptation and pigmentation in Y. pachychilus, and also supports broader phylogenomic and adaptive evolution studies across Gastromyzontidae.
Data availability
All raw sequencing reads from all libraries have been deposited in the NCBI Sequence Read Archive under accession number SRP636306. The genome assembly has been deposited in NCBI GenBank under accession number JBTNTC000000000.1 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_054948905.1). Annotation files are available via Figshare (https://doi.org/10.6084/m9.figshare.30403003.v4).
Code availability
All analyses were conducted with publicly available bioinformatics tools according to official guidelines, using default parameters unless noted otherwise. The core code is also available at https://github.com/wangliangkun501/Yaoshania_pachychilus/.
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Acknowledgements
We extend our sincere gratitude to the staff of the Management Center of the Dayao Mountain National Nature Reserve for their assistance. This study was funded by the Guangxi Natural Science Foundation under Grant No. 2026GXNSFBA00640092, the Project of Financial Funds of the Ministry of Agriculture and Rural Affairs: Investigation of Fishery Resources and Habitat in the Pearl River Basin (ZJZX-04), and Special survey on comprehensive scientific investigation of Guangxi Dayao Mountain National Nature Reserve (LKWT-2025-057).
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F.L., F.S. and D.P.W. conceived this project; F.L., J.S., C.X.L. and K.Q. collected samples; D.Y.W., Y.Q.H., and Y,S.L. prepared the sequencing samples; L.K.W. and F.S. analyzed the data; L.K.W. and F.L. wrote the manuscript; F.S., Z.Y.Y. and F.L. revised the manuscript. All authors have read and approved the final manuscript for publication.
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Lin, F., Wang, LK., Yuan, ZY. et al. A chromosome-level genome assembly of the panda loach (Yaoshania pachychilus). Sci Data (2026). https://doi.org/10.1038/s41597-026-07141-2
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DOI: https://doi.org/10.1038/s41597-026-07141-2
