Redistribution of RNA localization in early embryos of trout hybrid (Oncorhynchus mykiss egg fertilized with Salvelinus fontinalis sperm)

This study investigates the spatial transcriptomic dynamics during early embryogenesis in a hybrid trout, where the Oncorhynchus mykiss (rainbow trout) egg was fertilized with the Salvelinus fontinalis sperm. Using TOMO-seq, we profiled RNA localization along the animal–vegetal axis at key embryonic 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). Samples were collected in biological triplicates and sectioned into two sections (A & B) along the axis to assess spatial distribution. The data were used to analyze for de novo transcription by looking for paternal transcripts. Our results revealed spatially distinct transcriptome changes. 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 two distinct regions, labeled A and B, with region A representing the animal section and region B the vegetal section. This approach enabled the analysis of both temporal and spatial transcriptomic dynamics to uncover stage-specific transcriptomic changes occurring during the onset of embryogenesis with sepecific focus on detecting potential de novo transcriptions.