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bioRxiv · 10.64898/2026.07.17.738637

Title: A de novo transcriptomic atlas of early embryo development in the Arabian killifish

Akinmusola, R. Y.·Minhas, R.·O'Neill, P.·Kon-Nanjo, K.·Kon, T.·Shimada, Y.·Ramsdale, M.·Kudoh, T.
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Abstract

The Arabian killifish (Aphaniops dispar) is new tractable vertebrate model system for developmental, ecological and biomedical research, including drug screening, pharmacological and infection biology studies. It is a relatively small euryhaline teleost with broad thermal tolerance and adaptability across a wide range of salinities from freshwater to hypersaline habitats. The embryos and early larvae are tolerant to environmental stressors and exhibit a delayed period of nutritional independence before hatching. This advantage offers an extended window for experimenting on the early developmental processes. Here, we describe time-course gene expression profiling of Arabian killifish embryos across nine developmental time points, from the 1-cell stage to the larval pre-hatching stage. Clustering of dynamic expression profiles for 27,564 Trinity genes revealed coordinated transcriptional modules corresponding to the maternal, blastula, maternal-to-zygotic transition (MZT)-related, gastrulation, organogenesis and larval maturation stages. The maternal stage displayed a highly distinct expression profile, dominated by maternal-specific transcripts that are rapidly degraded during the MZT. The later stages, from 48 hpf onward, revealed a shift from early regulatory mechanisms to the expression of organogenesis-related genes. The ZGA stage showed the conserved up-regulation of many zinc finger-associated genes, consistent with zebrafish and other teleost genomes. Overall, embryo development in A. dispar is slower than in zebrafish, with equivalent stages occurring several hours later. We propose a delayed onset of zygotic genome activation (ZGA) in the blastula stage, corresponding to 6 hpf in the Arabian killifish. Taken together, this study provides a transcriptomic resource for mining embryo development-related genes in the Arabian killifish.

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Akinmusola, R. Y., Minhas, R., O'Neill, P., Kon-Nanjo, K., Kon, T., Shimada, Y., Ramsdale, M., Kudoh, T.. 2026-07-21. Title: A de novo transcriptomic atlas of early embryo development in the Arabian killifish. https://doi.org/10.64898/2026.07.17.738637

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