Genome-wide identification of candidate genes whose transcripts are locally expressed in early embryos of the spider Parasteatoda tepidariorum

The early embryo of the spider Parasteatoda tepidariorum initially shows spherical symmetry in morphology. Following a symmetry breaking event, it forms a radially symmetric germ disc in the hemisphere of the egg. In this work, we conducted RNA-sequencing of cells isolated from small different regions of radially symmetric forming/formed germ discs, aming to identify candidate genes whose transcripts are locally expressed in early spider embryos. Overall design: We isolated cells from small regions (central [c], peripheral [p], and intermediate [i]) of radially symmetric forming/formed germ discs at stage 3 (approximately 20 h after egg laying [AEL]), stage 4 (approximately 28-29 h AEL) and early stage 5 (approximately 31-32 h AEL) using glass capillary. We then conducted RNA-sequencing of the isolated cells to obtain transcriptomic data for comparison between different regions of the germ discs. Two or three biological replicates were obtained for each region for each stage. The RNAs were sequenced using the Illumina Miseq platform, and differentially expressed genes (DEGs) were evaluated in each comparison using EdgeR. The comparisons based on the early stage 5 samples allowed us to detect expected differences in gene expression between the central and peripheral regions of the germ disc (e.g., Pt-hh [aug3.g4322], Pt-lab [aug3.g7954], and Pt-opa [aug3.g12202]), which provided technical validation.