| Summary: | The phenotypic sex of fish is usually plastic. Low-temperature treatment induces the masculinization of <i>Takifugu rubripes</i>, resulting in pseudo-males (PM) with the physiological sex of a male (M) and genetic sex of a female (F). For a comparison of gonadal transcriptomes, we collected gonads from three groups of <i>T. rubripes</i> (F, M, and PM) for high-throughput transcriptome sequencing. The results provided 467,640,218 raw reads (70.15 Gb) and a total of 436,151,088 clean reads (65.43 Gb), with an average length of 150 bp. Only 79 differentially expressed genes (DEGs) were identified between F and PM, whereas 12,041 and 11,528 DEGs were identified between F and M, and PM and M, respectively. According to the functional annotation of DEGs, 13 DEGs related to gonadal development were screened (<i>LOC101066759</i>, <i>dgat1</i>, <i>limk1</i>, <i>fbxl3</i>, <i>col6a3</i>, <i>fgfr3</i>, <i>dusp22b</i>, <i>svil</i>, <i>abhd17b</i>, <i>srgap3</i>, <i>tmem88b</i>, <i>bud4</i>, and <i>mustn10</i>) which might participate in formating PM. A quantitative PCR of the DEGs confirmed the reliability of the RNA-seq. Our results provide an important contribution to the genome sequence resources for <i>T. rubripes</i> and insight into the molecular mechanism of masculinization in a cultured fish subject to low-temperature treatment.
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