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<p>The rainbow trout (<i>Oncorhynchus mykiss</i>) exhibits extensive karyotypic diversity (2n = 58–64) driven by Robertsonian translocations, yet widely used reference genomes are derived from North American lineages, leaving Chinese aquaculture populations underrepresented. Here, we present a near telomere-to-telomere (T2T) genome assembly of a farmed rainbow trout from China. Integrating PacBio HiFi, ONT ultra-long reads, and Hi-C&#xa0;data, we assembled a 2.29 Gb genome with 99.04% anchored to 30 chromosomes. Notably, the genome contains only 18 gaps, with 16 gap-free chromosomes and 13 achieving T2T status. Comparative synteny analysis revealed a third chromosomal fission/fusion iteration in which Swanson Omy14 splits into Arlee Omy14 and Omy32. Annotation identified 43,137 protein-coding genes, with a BUSCO completeness of 98.9%. This dataset provides a valuable resource for resolving lineage-specific structural variation, supporting pangenome construction and facilitating molecular breeding in rainbow trout.</p>

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Near telomere-to-telomere genome assembly of the rainbow trout (Oncorhynchus mykiss)

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年8月4日

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  • Shuhong Jiang,
  • Shuo Li,
  • Shenglei Han,
  • Chen Li,
  • Xuwen Cao,
  • Changlin Liu,
  • Chunlong Miao,
  • Caichao Dong,
  • Yanming Zhang,
  • Kaiqiang Liu,
  • Yuyan Liu,
  • Qian Wang,
  • Hong-yan Wang,
  • Changwei Shao

摘要

The rainbow trout (Oncorhynchus mykiss) exhibits extensive karyotypic diversity (2n = 58–64) driven by Robertsonian translocations, yet widely used reference genomes are derived from North American lineages, leaving Chinese aquaculture populations underrepresented. Here, we present a near telomere-to-telomere (T2T) genome assembly of a farmed rainbow trout from China. Integrating PacBio HiFi, ONT ultra-long reads, and Hi-C data, we assembled a 2.29 Gb genome with 99.04% anchored to 30 chromosomes. Notably, the genome contains only 18 gaps, with 16 gap-free chromosomes and 13 achieving T2T status. Comparative synteny analysis revealed a third chromosomal fission/fusion iteration in which Swanson Omy14 splits into Arlee Omy14 and Omy32. Annotation identified 43,137 protein-coding genes, with a BUSCO completeness of 98.9%. This dataset provides a valuable resource for resolving lineage-specific structural variation, supporting pangenome construction and facilitating molecular breeding in rainbow trout.