Transcriptomic analysis of marine medaka embryonic development

Marine medaka ( Oryzias melastigma ) has emerged as a valuable model organism for developmental biology and marine ecotoxicology. However, transcriptomic resources describing its normal embryonic development remain limited. This study aimed to characterize stage-dependent transcriptomic dynamics during marine medaka embryogenesis and to provide a developmental reference resource for this species. We performed time-series RNA sequencing across ten developmental stages, from the zygote stage to the pre-hatching period. Our analysis revealed dynamic non-linear transcriptomic transitions during embryogenesis and identified expression patterns consistent with a dual-wave architecture of zygotic genome activation (ZGA) during the maternal-to-zygotic transition (MZT). The early wave was associated mainly with chromatin-related and transcriptional regulatory functions, whereas the later wave was enriched for ribosome biogenesis and RNA processing. Network-based analyses identified candidate regulatory modules involving pluripotency-associated factors, maternal transcript clearance components, and stage-specific developmental gene sets. We also observed a transient ciliogenesis-associated expression program during the developmental window corresponding to Kupffer’s vesicle formation. Comparative summaries of ZGA timing, left-right asymmetry-related developmental timing, and key gene activation further place marine medaka embryogenesis in the context of other teleost models. This study provides a stage-resolved transcriptomic resource for normal embryonic development in marine medaka and identifies candidate gene expression programs associated with major developmental transitions. These data offer a useful framework for future functional, comparative, and exposure-related studies in this species.