Chromosome-Level Genome Assembly of the Sea Urchin Glyptocidaris crenularis and Sex Chromosome Identification

The economic importance of the sea urchin Glyptocidaris crenularis drives the need to elucidate the genetic mechanisms controlling its sex differentiation and development, a key step for enabling targeted genetic improvement. This study presents a chromosome-scale genome assembly for G. crenularis characterized by 22 chromosome-length scaffolds and a total length of 787.45 Mb. The phylogenetic tree revealed that G. crenularis diverged early among sea urchins. Synteny analysis among species suggested that superscaffold 10 might be the sex chromosome. Subsequent transcriptomic profiling further revealed 273 genes (298 transcripts) on chromosome 10 whose expression differed significantly between testis and ovary tissues. The genomic resources established in this study provide a foundation for investigating the population genetics, evolution, and functional mechanisms of this species, while the identified sex chromosomes and candidate genes pave the way for elucidating the molecular basis of sex determination in sea urchins.