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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #420562
Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: Tracing 100 million years of gene evolution following whole genome duplication in rainbow trout

Author
item ALI, ALI - US Department Of Agriculture (USDA)
item Gao, Guangtu
item AL-TOBASEI, RAFET - Middle Tennessee State University
item YOUNGBLOOD, RAMEY - Mississippi State University
item Waldbieser, Geoffrey
item Scheffler, Brian
item HUAIJUN, ZHOU - University Of California, Davis
item Palti, Yniv
item SALEM, MOHAMED - University Of Maryland

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2024
Publication Date: 1/10/2025
Citation: Ali, A., Gao, G., Al-Tobasei, R., Youngblood, R., Waldbieser, G.C., Scheffler, B.E., Huaijun, Z., Palti, Y., Salem, M. 2025. Tracing 100 million years of gene evolution following whole genome duplication in rainbow trout. Plant and Animal Genome Conference. Paper No. 130.

Interpretive Summary:

Technical Abstract: In this study, we improved the rainbow trout (Oncorhynchus mykiss) reference genome to explore the evolutionary fate of duplicate genes following the whole-genome duplication (WGD) event in salmonids. Our results highlight the critical role of the independent model in the long-term evolution of alternative splicing (AS), with ohnologues gradually shifting towards reduced splicing diversity as evolutionary time progresses. Further, gene pairs under relaxed purifying selection pressure tend to acquire novel functions. Neofunctionalized and independently splicing gene pairs exhibit distinct epigenetic landscapes, marked by significant divergence in histone modification patterns. Notably, H3K27ac, a marker of active enhancers, displayed the most significant divergence between neofunctionalized and independent gene pairs, indicating a crucial role for enhancers in driving the functional divergence of ohnologues following WGD. This study sheds new light on the evolutionary dynamics of gene duplication and their regulatory landscapes, providing critical insights into how epigenetic modifications contribute to the retention and functional innovation of duplicated genes while mitigating the fitness challenges posed by genome duplication.