De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference

Ali, A. R.; Waldbieser, G. C.; Youngblood, R. C.; Wheeler, P. A.; Scheffler, B.; Willis, S.; Narum, S. R.; Thorgaard, G. H.; Salem, M.; Palti, Y.

doi:10.1101/2025.10.11.681701

bioRxiv · 10.1101/2025.10.11.681701

De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference

Ali, A. R.·Waldbieser, G. C.·Youngblood, R. C.·Wheeler, P. A.·Scheffler, B.·Willis, S.·Narum, S. R.·Thorgaard, G. H.·Salem, M.·Palti, Y.

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Abstract

Rainbow trout (Oncorhynchus mykiss) exhibit extensive 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, interior Columbia Basin), along with the previously published assemblies of the Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska) lines. All assemblies provide nearly complete coverage of known genes (BUSCO 95.8-99.7%) and are similar in genome size ([~]2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Comparative whole-genome alignments revealed high sequence conservation (97-98% identity) among assemblies, but also evidence of extensive structural variation of at least 50 bp in length. Structural variant (SV) profiling identified tens of thousands of deletions, insertions, and complex rearrangements largely in noncoding sequences. In an initial assessment of the utility of having multiple de novo genome assemblies for rainbow trout, we found that two strains (Arlee and Swanson; domesticated) share SVs enriched in genes linked with growth, reproduction, and adaptation to domestication, such as GTP binding and ECM-receptor interaction. In comparison, the other two strains (WR and KC; wild origin) 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/ER{beta}-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.

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Ali, A. R., Waldbieser, G. C., Youngblood, R. C., Wheeler, P. A., Scheffler, B., Willis, S., Narum, S. R., Thorgaard, G. H., Salem, M., Palti, Y.. 2025-10-13. De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference. https://doi.org/10.1101/2025.10.11.681701

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