De novo genome assemblies of four rainbow trout genetic lines reveal structural variants in pursuit of a pangenome reference

Authors: ALI, ALI - University Of Maryland; Waldbieser, Geoffrey; YOUNGBLOOD, RAMEY - Mississippi State University; WEELER, PAUL - Washington State University; Scheffler, Brian; WILLIS, STUART - Columbia River Intertribal Fish Commission; NARUM, SHAWN - Columbia River Intertribal Fish Commission; TORGAARD, GARY - Washington State University; SALEM, MOHAMED - University Of Maryland; Palti, Yniv

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2026
Publication Date: 6/17/2026
Citation: Ali, A.R., Waldbieser, G.C., Youngblood, R., Weeler, P., Scheffler, B.E., Willis, S., Narum, S., Torgaard, G., Salem, M., Palti, Y. 2026. De novo genome assemblies of four rainbow trout genetic lines reveal structural variants in pursuit of a pangenome reference. Molecular Ecology Resources. 26. Article 70167. https://doi.org/10.1111/1755-0998.70167.
DOI: https://doi.org/10.1111/1755-0998.70167

Interpretive Summary: A high-quality reference physical genome map is important for facilitating meaningful genetic analyses and enhancing research on the physiology of the organism or species. In an effort to improve the rainbow trout reference genome assembly, we used recent improvements in DNA sequencing technology and bioinformatics to generate two additional reference genome assemblies for rainbow trout. Due to the large genetic and genomic diversity within this species it is important to generate multiple high quality reference genome maps that represent most of the genetic diversity within the species. Towards this goal of generating a pan-genome reference for rainbow trout we have previously generated high quality genome maps from the rainbow trout Arlee and Swanson lines. Here we report on the generation of high quality genome assemblies for the Whale Rock and Keitlhey Creek lines which add representation of wild populations from the coastal and inland lineages of rainbow trout to the developing reference pan-genome. In a proof-of-concept analysis to demonstrate the utility of having multiple de-novo genome assemblies for rainbow trout, we identified a large number of structural variations in the genome with potential profound implications on diversity of gene expression and functional impact on traits of interest. Together, these genome assemblies and their comparative analyses establish a foundation for a rainbow trout pan-genome reference, illuminating how they can be utilized to reveal the genetic basis of domestication, adaptation, and other complex traits in rainbow trout. The study demonstrated that the generation of multiple genome resources for research in rainbow trout is crucial for basic and applied research on this iconic species for aquaculture, sport fishing, fisheries and cultural heritage in the US.

Technical Abstract: Rainbow trout (Oncorhynchus mykiss) exhibit extensive genetic and genomic diversity shaped by domestication, life history, and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemblies of two genetically and ecologically distinct lines: Whale Rock (WR; wild, landlocked, Central California) and Keithley Creek (KC; wild, resident, Columbia Basin), along with previously published assemblies of Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska). All assemblies are almost complete (BUSCO 95.8–99.7%) and similar in size (~2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Whole-genome alignments reveal high sequence conservation (97–98% identity) alongside extensive structural variation (SV). SV profiling identified tens of thousands of deletions, insertions, and complex rearrangements in largely noncoding sequences. In a proof-of-concept analysis to demonstrate the utility of having multiple de-novo genome assemblies for rainbow trout we found that the two domesticated strains (Arlee and Swanson) share structural variants (SVs) enriched in genes linked with growth, reproduction, and captivity adaptation, such as GTP binding and ECM-receptor interaction. In comparison, the two wild strains (WR and KC) share SVs associated with reproductive timing such as GnRH signaling pathway. Both Arlee and WR also have unique SVs potentially related to their geographic origin and unique life history. Additionally, we identified SVs in key regions, such as a QTL for fillet yield on Omy17 and the maturation-associated SIX6/ERß-GPHB5 locus on Omy25q, suggesting the importance of considering SVs when investigating the genomics of complex traits. Together, these assemblies and comparative analyses establish a foundation for a rainbow trout pangenome reference, illuminating how they can be utilized to reveal the structural genomic basis of domestication, adaptation, and other complex traits in O. mykiss.