# An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

## TL;DR

This study creates a detailed cell atlas of spider embryos using single-cell RNA sequencing, revealing new insights into spider development and arthropod evolution.

## Contribution

The study provides the first single-cell transcriptomic atlas of spider embryos, revealing novel gene expression patterns and cell types.

## Key findings

- Single-cell RNA sequencing identified 20 distinct cell clusters marked by developmental genes in spider embryos.
- Hox gene ohnologs were found in different cell clusters, suggesting sub- or neo-functionalization after genome duplication.
- The atlas reveals new insights into head patterning, limb development, and gut development in spider embryos.

## Abstract

Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5 k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. We found differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We identified many Hox genes as markers of cell clusters, and Hox gene ohnologs were often present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in an arachnopulmonate ancestor (spiders, scorpions, and related orders). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution.

The online version contains supplementary material available at 10.1186/s13227-024-00224-4.