Background: Early sex differentiation genes of zebrafish remain an unsolved mystery due to the difficulty to distinguish the sex of juvenile zebrafish. However, aromatase inhibitors (AIs) could direct juvenile zebrafish sex differentiation to male and even induce ovary-to-testis reversal in adult zebrafish. Results: In order to determine the transcriptomic changes of sex differentiation in juvenile zebrafish and early sexreversal in adult zebrafish, we sequenced the transcriptomes of juvenile and adult zebrafish treated with AI exemestane (EM) for 32 days, when juvenile zebrafish sex differentiation finished. EM treatment in females upregulated the expression of genes involved in estrogen metabolic process, female gamete generation and oogenesis, including gsdf, macf1a and paqr5a, while down-regulated the expression of vitellogenin (vtg) genes, including vtg6, vtg2, vtg4, and vtg7 due to the lower level of Estradiol (E2). Furthermore, EM-juveniles showed upregulation in genes related to cell death and apoptosis, such as bcl2l16 and anax1c, while the control-juveniles exhibited up-regulation of genes involved in positive regulation of reproductive process and oocyte differentiation such as zar1 and zpcx. Moreover, EM-females showed higher enrichment than control females in genes involved in VEGF signaling pathway, glycosaminoglycan degradation, hedgehog signaling pathway, GnRH signaling pathway and steroid hormone biosynthesis. Conclusions:Our study shows anti-masculinization in EM-treated adult females but not in EM-treated juveniles. This may be responsible for the lower sex plasticity in adults than juveniles.

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Maintenance and differentiation of germline stem and progenitor cells (GSPCs) is important for sexual reproduction. Here, the authors identify zebrafish pld6 as a novel germline-specific gene by cross-analyzing different RNA sequencing results, and find that pld6 knockout mutants develop exclusively into infertile males. In pld6 mutants, GSPCs fail to differentiate and undergo apoptosis, leading to masculinization and infertility. Mitochondrial fusion in pld6-depleted GSPCs is severely impaired, and the mutants exhibit defects in piRNA biogenesis and transposon suppression. Overall, this work uncovers zebrafish Pld6 as a novel germline-specific regulator of mitochondrial fusion, and highlights its essential role in the maintenance and differentiation of GSPCs as well as gonadal development and gametogenesis.

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their own network in the genomes, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific gene, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically dated the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using protein-family-based pipeline with Wagner parsimony algorithm. We also collected gene age estimate data from other studies and uniformed the gene age estimates to time ranges in million years for comparison across studies. All the data were cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, was provided to researchers for exploring gene functions.

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Zebrafish (Danio rerio) has been used as a promising animal model to study gonadal development and gametogenesis. Although previous studies have identified critical molecules participating in zebrafish gonad differentiation, a landscape view of the biological processes involved in this process is still lacking. Here we isolated intact zebrafish differentiating gonads, at 25 days post-fertilization (dpf) and 30 dpf, and conducted RNA-seq analysis between the juvenile gonads that tended to develop into ovaries or testes. Our study demonstrates that the juvenile ovary and testis at 25 dpf and 30 dpf are different at the level of biological process. During ovary differentiation, the biological processes related to metabolic activities in production of energy and maternal substances, RNA degradation, and DNA repair were enriched. During testis differentiation, the biological processes related to cell proliferation, differentiation, and morphogenesis were enriched, with a total of 15 signaling pathways. Notably, we reveal that the immune-related processes are extensively involved in the regulation of testis development. Overall, this study provides a landscape of differentiated biological processes and novel insights into the initiation of sex differentiation in zebrafish.