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Simple Summary  Spot-fin porcupine fish ( Diodon hystrix ) has been recognized as a new and emerging aquaculture species with promising economic value in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a major technological barrier for the development of large-scale aquaculture of  D. hystrix . In this study, the first gonad transcriptomes of  D. hystrix  were analyzed using Illumina HiSeq sequencing. Comparison of ovary and testis transcriptomes identified a set of differentially expressed genes (DEGs) supposed to be associated with gonadal development and gametogenesis. The conserved expression profiles of the well-known reproduction-related genes implies their similar roles in gonad differentiation and development in  D. hystrix . The detailed transcriptome data can improve our understanding of the regulatory functions of sex-related genes in  D. hystrix .    Abstract   Diodon hystrix  is a new and emerging aquaculture species in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a barrier for the commercial aquaculture of  D. hystrix . More genetic information is needed to identify genes critical for gonadal development. Here, the first gonadal transcriptomes of  D. hystrix  were analyzed and 151.89 million clean reads were generated. All reads were assembled into 57,077 unigenes, and 24,574 could be annotated. By comparing the gonad transcriptomes, 11,487 differentially expressed genes were obtained, of which 4599 were upregulated and 6888 were downregulated in the ovaries. Using enrichment analyses, many functional pathways were found to be associated with reproduction regulation. A set of sex-biased genes putatively involved in gonad development and gametogenesis were identified and their sexually dimorphic expression patterns were characterized. The detailed transcriptomic data provide a useful resource for further research on  D. hystrix  reproductive manipulation.

Comparison of Gonadal Transcriptomes Uncovers Reproduction-Related Genes with Sexually Dimorphic Expression Patterns in Diodon hystrix