Abstract
Freshwater Gammarus species represent important keystone organisms in aquatic ecosystems, and are sensitive to environmental changes. Here, we present the first pseudo-chromosome-level genome of Gammarus nekkensis, endemic to north China. We integrated PacBio HiFi long-read sequencing, Illumina short-read sequencing, and Hi-C scaffolding to generate a high-quality, pseudo-chromosome-scale genome assembly. The assembled genome is approximately 6.24 Gb in size, with a scaffold N50 of 233.63 Mb, and 96.76% of the sequences were successfully anchored to 26 pseudo-chromosomes. A total of 39,474 protein-coding genes were predicted, and approximately 70% of these genes obtained functional annotations. Repetitive elements constituted about 63.93% of the genome, with long interspersed nuclear elements (LINE) being the most abundant (23.98%). BUSCO analysis indicated that both the assembly and annotation are highly complete compared with published amphipod genomes. This high-quality genome enables studies of sex determination, adaptive evolution, and genomic diversity in G. nekkensis, with applications for its conservation and breeding.
Data availability
The raw sequencing data supporting this study have been deposited in the European Nucleotide Archive (ENA) with the following accession numbers: PacBio data, ERR16720729, Illumina data, ERR16722743, and Hi-C data, ERR16729500. The assembled genome sequence is available from the ENA under accession number ERZ29160471 (GCA_980912865) and from the China National GeneBank under accession number CNA0509588. The functional annotation information of the gene was uploaded to Figshare database under the following: https://doi.org/10.6084/m9.figshare.31698019.
Code availability
All analyses were conducted using the software and pipelines as specified in the Methods section, without the generation of any custom code.
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Acknowledgements
This study was supported by the National Natural Science Foundation of China (grant number 32470474, 32500387), the International Partnership Program of Chinese Academy of Sciences (grant number 073GJHZ2024043MI), the Institute of Zoology, Chinese Academy of Sciences (2023IOZ0104, 2024IOZ0108); Beijing Natural Science Foundation (grant number 5244045).
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D.L. and Z.H. conceived the study; D.L., Z.L. and H.L. collected sample; Y.T., H.L. and Z.L. dissected the tissue and sent the separated samples to the sequencing company; The genome assembly, annotation, and analysis are completed by D.L.; C.-D.Z. provided guidance and suggestions for the writing and conceptualization of this article; The final manuscript has been read, edited, and approved by all authors.
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Lu, D., Liu, H., Tong, Y. et al. An annotated genome of freshwater amphipod (Gammarus nekkensis). Sci Data (2026). https://doi.org/10.1038/s41597-026-07126-1
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DOI: https://doi.org/10.1038/s41597-026-07126-1
