Redistribution of RNA localization in early embryos of rainbow trout

This study investigates spatial transcriptomic dynamics during early embryogenesis in Oncorhynchus mykiss (rainbow trout), a teleost species with large oocytes and prolonged developmental timing. Using TOMO-seq, we profiled RNA localization along the animal–vegetal axis at key embryonic stages, including 0 hpf (freshly fertilized egg/zygote), 1 hpf (early cleavage stage), 1 dpf (early blastula stage, ~32-64 cells), and 3 dpf (mid-blastula, ~1000 cells). Samples were collected in biological triplicates and sectioned into five defined regions (A–E) along the axis to assess spatial distribution. The data were used to analyze maternal RNA localization, transcript stability, and onset of zygotic transcription. Our results reveal spatially distinct transcriptome changes, highlighting both conserved and species-specific mechanisms relative to other teleosts such as zebrafish. Overall design: To investigate transcriptomic changes during early embryonic development, TOMO-seq was applied to a series of developmental stages: 0 hpf (freshly fertilized egg/zygote), 1 hpf (early cleavage stage), 1 dpf (early blastula stage, ~32-64 cells), and 3 dpf (mid-blastula, ~1000 cells). Biological triplicates were used for each condition. Samples were sectioned along the animal–vegetal axis into five distinct regions, labeled A through E, with region A representing the most animal and region E the most vegetal portion. This approach enabled the analysis of both temporal and spatial transcriptomic dynamics to uncover stage-specific transcriptomic changes occurring during the onset of embryogenesis.