Utilizing Next-Generation Sequencing to Develop and Characterize Microsatellite Loci in Cuttlefish (Sepia pharaonis) and Cross-Amplification in Other Sepiidaes

The cuttlefish Sepia pharaonis, known for its economic value, is distributed in the tropical coastal waters of the Indo-pacific region. In this study, we developed twenty-one microsatellite loci for S. pharaonis through next-generation sequencing technology. A total of 100 alleles were detected, and the number of alleles per loci ranged from 2 to 9. The observed and expected heterozygosities per loci ranged from 0.000 to 0.531 and from 0.031 to 0.751, respectively. Polymorphism information content (PIC) showed that six loci were highly informative (PIC > 0.5). Five loci (CL1142, CL1770, CL2683, CL3494, CL 3674) significantly deviated from the Hardy-Weinberg equilibrium after a Bonferroni correction (P < 0.05), and none of the loci showed linkage disequilibrium. In addition, these loci were cross-amplified in three closelyrelated species. Nineteen, fifteen, and thirteen loci were amplified in Sepia lycidas, Sepia esculenta and Sepiella japonica, respectively.