Comparative RNA-Seq analysis of differentially expressed genes in the testis and ovary of Takifugu rubripes

Abstract Takifugu rubripes is a classical model organism for studying the role of gonad organogenesis in such physiological processes as fertilization, sex determination, and sexual development. To explicitly investigate the mechanism associated with gonad organogenesis in T. rubripes , we obtained 44.3 million and 55.2 million raw reads from the testis and ovary, respectively, by RNA-seq and from these, 18,523 genes were identified. A total of 680 differentially expressed genes were obtained from comparison transcriptome analysis between the testis and ovary, and of these, 556 genes were up-regulated in the testis, whereas only 124 genes were upregulated in the ovary. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many of these genes encode proteins involved in signal transduction and gonad development. We mainly focused on the differentially expressed genes that have the potential to develop into the gonad. The generation of large scale transcriptomic data presented in this work would enrich the genetic resources of T. rubripes , which should be valuable to the comparative and evolutionary studies of teleosts.