Genome-wide quantitative dissection of an arthropod segmented body plan at single-cell resolution

Developmental processes underlying the characteristic segmented body plans in arthropods vary widely. While Drosophila is well-studied, few other arthropod species offer platforms for comparable genomics at single-cell resolution. Here, we present high-quality quantitative data from single-nucleus RNA sequencing of spider Parasteatoda tepidariorum embryos at late stage 5 and stage 7, a critical period of emergence of segmental units along the anterior-posterior (AP) axis. Clustering analysis of the stage-7 dataset reconstructs an axial alignment of ectoderm cells, reflecting the differing cell states along the segmenting AP axis. This enables us to obtain genome-wide quantitative gene expression profiles along the reconstructed axis, which were used for unbiased and thorough molecular investigation of pattern elements employing statistical methods. Comprehensive gene-to-gene correlation analyses suggest distinct gene-regulatory interactions in different regions along the reconstructed axis. This study lays the foundation for exploring the origins of developmental diversity in the arthropod body plan.