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<p>Freshwater <i>Gammarus</i> species represent important keystone organisms in aquatic ecosystems, and are sensitive to environmental changes. Here, we present the first pseudo-chromosome-level genome of <i>Gammarus nekkensis</i>, 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 <i>G. nekkensis</i>, with applications for its conservation and breeding.</p>

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An annotated genome of freshwater amphipod (Gammarus nekkensis)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月2日

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  • Decai Lu,
  • Hongguang Liu,
  • Yan Tong,
  • Zeyu Liu,
  • Chao-Dong Zhu,
  • Zhonge Hou

摘要

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.