Genome-wide identification, evolutionary diversification and developmental expression of the Sox gene family in three brachyuran crabs

The Sox (SRY-related HMG-box) transcription factor family plays central roles in cell fate determination, neurogenesis, and reproductive development, yet its evolutionary history and molecular diversification in crustaceans remain poorly understood. Here we present a genome-wide comparative study of Sox genes in three representative crabs—Portunus trituberculatus, Scylla paramamosain, and Eriocheir sinensis—based on their high-quality reference genomes. We identified 16, 16, and 15 Sox genes, respectively, and established a robust HMG-box–based phylogeny and nomenclature, assigning all members to the canonical B–F subgroups and an ungrouped Sox-like clade. Comparative analyses uncovered striking lineage-specific events, including the complete loss of SoxB1 in E. sinensis and an expansion of the SoxC subgroup, accompanied by a mosaic of deeply conserved and newly derived motifs and domains. Integrative transcriptomic analyses revealed that many Sox genes are strongly expressed in neural tissues and testes, and that certain SoxB and SoxC members exhibit stage-specific activation during embryonic, larval, or testicular development, highlighting key roles in neurogenesis, pluripotency maintenance, and spermatogenesis. Together, these findings provide the first comprehensive evolutionary framework for the crab Sox family, uncover unexpected gene loss and subgroup expansion, and offer new insights into how conserved transcriptional regulators diversify to shape neural and reproductive programs in arthropods.