Chromosome-level Assembly of the Genome of Mesocentrotus nudus Reveals a Sex-Linked Region on Chromosome 7.

The sea urchin Mesocentrotus nudus holds significant economic importance, making a comprehensive understanding of its sex differentiation and development mechanisms crucial for facilitating genetic enhancement. In this study, a high-quality chromosome-level assembly of the M. nudus genome was accomplished, spanning 707 Mb and encompassing 21 chromosomes, which together represented 97.6% of the assembly. Analysis of the locations of sex-linked markers indicated that sex determination in M. nudus may be predominantly governed by a confined region on chromosome 7. Within this specific area, an initial screening identified 37 protein-coding genes, encompassing 64 transcripts. Subsequent comparative transcriptome analysis revealed notable differences in the expression patterns of 11 genes (comprising 12 transcripts) between the testes and ovaries of M. nudus. In conclusion, this genome assembly serves as an invaluable resource for future investigations into the population genetics, evolutionary history, and genetic mechanism analysis of M. nudus. Moreover, the identification of the genomic location of the sex-linked region in M. nudus, coupled with the identification of candidate sex-determining genes, lends further credence to the notion of rapid evolution in sex-determining mechanisms among sea urchins.