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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #407483
Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: Chromosome-level genome assembly and annotation of the Swanson rainbow trout homozygous line

Author
item ALI, ALI - University Of Maryland
item Gao, Guangtu
item AL-TOBASEI, RAFET - Middle Tennessee State University
item YOUNGBLOOD, RAMEY - Mississippi State University
item Waldbieser, Geoffrey
item Scheffler, Brian
item Palti, Yniv
item SALEM, MOHAMED - University Of Maryland

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2025
Publication Date: 2/26/2025
Citation: Ali, A., Gao, G., Al-Tobasei, R., Youngblood, R., Waldbieser, G.C., Scheffler, B.E., Palti, Y., Salem, M. 2025. Chromosome-level genome assembly and annotation of the Swanson rainbow trout homozygous line. Scientific Data. 12:345(2025). https://doi.org/10.1038/s41597-025-04693-7.
DOI: https://doi.org/10.1038/s41597-025-04693-7

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 a new and improved reference genome assembly for rainbow trout. Due to the large genetic and genomic diversity within species it is important to generate multiple high quality reference genome maps that represent most of genetic diversity within the species. Towards this goal of generating a pan-genome reference for rainbow trout we have previously generated high quality genome map from the rainbow trout Arlee line. Here we improved the assembly and annotation of the rainbow trout reference genome from the Swanson genetic line and used it to understand the early evolutionary fate of duplicated gene copies following whole-genome duplication. Our results challenge recent claims in the literature that the effect of duplication on alternative splicing of genes is limited and help resolve conflicted theories on the inverse relationship between gene duplication and splicing. 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: In this study, we utilized an improved reference genome for rainbow trout to investigate the fate of duplicate genes following the whole genome duplication (WGD) event in salmonids. Our work showed clear evidence of transitioning from evolutionary-dependent to independent mechanisms of alternative splicing (AS) and gene duplication after WGD. The study demonstrated that ohnologues, duplicated genes originating from WGD, undergo an initial phase of accelerated splicing in early evolution to balance gene dosage. However, our observations also suggest that splice variants are lost at an increased rate as evolutionary time progresses, potentially due to relaxed purifying selection pressure. Our findings highlight the role of the independent model in the long-term evolutionary trajectory of AS. Additionally, we discovered that evolutionarily old ohnologues or those with low levels of ancestral splicing tend to acquire novel and distinct functions. Independent and neo-functionalized gene pairs display divergent histone-modification epigenetic landscapes, which regulate the binding of splicing factors to pre-mRNAs. Our results provide novel insights into the evolutionary dynamics of duplicate genes and their regulatory elements, which help alleviate the fitness costs posed by genome doubling.