The segmented body plan of arthropods, from insects to spiders, has long fascinated biologists for its conserved appearance and diverse developmental origins. While the fruit fly has been studied extensively, other arthropods have remained less understood at a comparable genomic scale. A new study changes this by applying advanced single-cell technologies, which capture the activity of individual cells one by one, to unravel how segmentation emerges in the common house spider, Parasteatoda tepidariorum.
The research was conducted by Takanori Akaiwa, Dr. Hiroki Oda, and Dr. Yasuko Akiyama-Oda from JT Biohistory Resesarch Hall, Osaka University, and Osaka Medical and Pharmaceutical University. Their findings published in Communications Biology. Using single-nucleus RNA sequencing, a technique that measures which genes are transcribed in the nucleus of each cell, the team generated a detailed molecular map of spider embryos at critical stages of segmentation along the anterior–posterior axis, meaning from head to tail.
By examining cell states at single-cell resolution, or viewing development at the level of each individual cell, the researchers were able to observe patterns that mirror the emergence of repeating body segments. This revealed how ectodermal cells, which later give rise to epidermis and nervous tissue, align in ways that correspond with head, thorax, and posterior regions. In practical terms, they demonstrated that the dynamically established gene expression patterns—the instructions from DNA that turn on and off—could be visualized and quantified across thousands of cells. Some patterns appeared as region-specific domains, others as stripes generated by wave-like splitting and oscillation, all of which contribute to shaping the spider’s body. This showed that even though arthropods share a segmented body, the molecular steps differ substantially across species.
One of the key breakthroughs of the research was the ability to reconstruct the axial alignment of spider cells, essentially recreating the body’s blueprint from head to tail, solely from molecular data. Alignment along this axis is what allows the correct sequence of body parts to emerge. As Dr. Akiyama-Oda explained, “Reconstruction of an axial pattern using only data derived from single-nucleus sequencing has not been reported in other animals. Our key observations indicate a polarized state of the ectoderm cells, establishing a foundation for stripe formation.” This demonstrates how spiders provide a powerful model for studying segmentation beyond the fruit fly.
The study also identified novel cell states in the mesoderm, the layer that forms muscles and internal organs, and in the endoderm, which produces the gut and related tissues. These findings highlight cellular diversity during development. Importantly, the team’s analysis revealed over two hundred genes that could mathematically reconstruct the segmental stripe patterns, a finding that could help build predictive models of embryonic development. Predictive models are simplified representations that allow scientists to test ideas and forecast outcomes of biological processes. As Dr. Akiyama-Oda noted, “The high-resolution, quantitative single-nucleus data generated here provide a robust foundation for understanding the diverse mechanisms underlying arthropod segmentation and connect directly to mathematical modeling of cell-based processes.”.
The implications of this research extend well beyond spiders. Akaiwa, Dr. Oda, and Dr. Akiyama-Oda emphasize that by demonstrating that detailed gene expression landscapes, or maps of how genes are active across the body, can be built without relying on established models like fruit flies, their study opens opportunities to explore the origins of developmental diversity across the animal kingdom. It suggests that segmentation, though conserved in outcome, is achieved by multiple routes—underscoring evolution’s flexibility in shaping life’s fundamental patterns.
Journal Reference
Akaiwa T., Oda H., Akiyama-Oda Y. “Genome-wide quantitative dissection of an arthropod segmented body plan at single-cell resolution.” Communications Biology, 2025; 8:913. DOI: https://doi.org/10.1038/s42003-025-08335-x
About the Authors
Takanori Akaiwa is an emerging scientist specializing in developmental, cell, and molecular biology. He graduated from the master’s program at the Graduate School of Science, Kyoto University and went on to the doctoral program at the Graduate School of Science, Osaka University, where he joined Oda’s laboratory at JT Biohistory Research Hall. Mr. Akaiwa became interested in the “spider developmental biology” project in Oda’s laboratory. He worked together with Dr. Yasuko Akiyama-Oda to apply single-cell and single-nucleus RNA-sequencing techniques to Parasteatoda tepidariorum spider embryos. He not only obtained high-quality datasets but also developed computational techniques, such as R and Python, to analyze the datasets. His efforts contributed to demonstrating the power of single-nucleus RNA-sequencing in spider developmental biology. He is now preparing his doctoral thesis.
Dr. Hiroki Oda is a scientist and group leader at JT Biohistory Research Hall and also a guest professor at the Graduate School of Science, Osaka University. He is working in intersecting fields of cell, developmental and evolutionary biology. His work focuses on understanding the origins of animal diversity as well as key changes or transitions in cell and developmental systems. He originally studied cell-cell adhesion systems using Drosophila melanogaster, but has expanded his scope to a wider range of animals, including spiders, since 2000. He started, together with Dr. Yasuko Akiyama-Oda, spider developmental biology using the species Parasteatoda tepidariorum and demonstrated the power of this spider as a model organism, especially in chelicerate arthropods. He has contributed to technical developments with the spider as well as enhancing evo-devo studies.
Dr. Yasuko Akiyama-Oda is a scientist at JT Biohistory Research Hall and also belongs to Osaka Medical and Pharmaceutical University. She works in the field of developmental and evolutionary biology, with a focus on early embryogenesis of arthropods. After originally studying mechanisms of cell differentiation in the Drosophila melanogaster embryo, she became interested in the diversity of developmental systems. Around 2000, together with Dr. Hiroki Oda, she began studying the early development of the common house spider Parasteatoda tepidariorum, and found that there is a symmetry-breaking source of secreted signals in the early spider embryo. She successfully applied parental RNA interference to analyze gene functions in Parasteatoda embryos, which laid the foundation for this spider species to emerge as a key model organism in arthropods. A series of her work has highlighted the contrasting mechanisms of early development between spiders and fruit flies, and she continues to promote genome-wide studies to further elucidate arthropod developmental diversity.
