Background: We previously discovered a potential sex-specific single nucleotide polymorphism (SNP) locus named SNP1888 in mud crab (Scylla paramamosain). Methods: In this study, we first verified SNP1888 to be truly a female-specific locus and then we identified a novel imprinted gene (designated as Sp-Pol) at the upstream of SNP1888 (SNP1888 is located at the 3'-UTR of Sp-Pol). Moreover, SNP1888 together with Sp-Pol were mapped on LG32 of a high-density genetic map. Results: Phylogenetic

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... is showed that Sp-Pol may need to be classified as a new gene family due to the very low sequence identity with other known genes. Sp-Pol was expressed at a higher level in gonads compared to other tissues and its expression level in the testis was much higher than in the ovary. Coincidentally, mono-allelic expression was observed in the ovary. Moreover, Sp-Pol exhibited sex-biased expression with approximately 3- to 4-fold higher in males than in females at fifth (C5) and sixth (C6) crablet stages. During the zoeae development, Sp-Pol had the highest expression at the zoea I stage. After unilateral eyestalk ablation, the expression level of Sp-Pol significantly increased in testis and hepatopancreas in males, while it was downregulated in the hepatopancreas of females. Fluorescence in situ hybridization (FISH) assay revealed that Sp-Pol transcripts were strongly localized in the epithelia of seminiferous tubules of the testis and in the ovary it was detected in the oogonium cells.Conclusion: These results demonstrated that Sp-Pol may play important roles in the sexual development of S. paramamosain.