Stage-resolved transcriptomic analysis of GPCR expression during settlement and metamorphosis in the sea urchin...

Larval settlement and metamorphosis are critical developmental transitions in sea urchins and represent a major bottleneck in aquaculture. Here, we used stage-resolved transcriptome sequencing to characterize genome-wide gene expression dynamics during settlement and metamorphosis in the purple sea urchin Heliocidaris crassispina, with a particular focus on G protein-coupled receptors (GPCRs). Based on a refined chromosome-level genome annotation, 763 GPCR candidate genes were identified and their expression patterns were systematically examined across six-arm larvae, eight-arm competent larvae, and early juveniles. Transcriptomic analyses revealed pronounced stage-dependent remodeling, with the competent larval stage showing a marked expansion of expressed GPCRs. Time-series clustering identified two major GPCR expression patterns: one associated with the competence stage and characterized by transient or peak-shaped upregulation, and another that became more prominent after settlement and remained highly expressed in early juveniles. PPI network analysis further suggested that these temporal patterns were associated with coordinated network organization rather than isolated receptor-level changes. Representative GPCR expression patterns were independently validated by qRT-PCR. These results provide a stage-resolved transcriptomic framework for understanding GPCR expression dynamics during sea urchin settlement and metamorphosis and offer a basis for future functional studies in echinoderms.