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PolyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf

ABSTRACT: In this study, we explored the biological process of zebrafish gonad differentiation through Poly(A)-enriched RNA sequencing，and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification, it is found that, in the differentiating ovary, the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway, indicating that oocyte requires the accumulation of maternal RNA, protein, sugar, lipids, vitamins and other substances, which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition, during ovarian differentiation, the biological processes associated with the nucleus, mitochondria, and cytoplasmic particles are more active, and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary, when the gonad differentiates into testis, the differentially expressed genes are more enriched in biological regulation and development processes, including morphogenesis, cell proliferation, etc.The cytometers adapted to these biological processes are associated with cell membrane, such as membrane receptors, extra-cellular regions, extra-cellular matrix, and cell connections, and also associated with nuclear chromatin. In addition, we enriched 14 signaling pathways involved in testis differentiation, and showed the expression heat map of every differentially expressed gene of each pathway. Overall, the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis, helping us to get a comprehensive understanding of the basis on biological events and molecules during this process.

ORGANISM(S): Danio rerio

PROVIDER: GSE175979 | GEO | 2022/05/18

REPOSITORIES: GEO

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Project description:African clawed frog Xenopus sp. is used extensively for developmental biology and toxicology research. Amid concerns of environmental pollutants disrupting endocrine systems and causing altered reproductive development in wildlife, eco-toxicology research has led to a focus on linking molecular initiating events to population-level effects. As such, efforts to better understand reproductive development at the molecular level in these model species are warranted. To that end, transcriptomes were characterized in differentiating Xenopus tropicalis gonad tissues at Nieuwkoop and Faber (NF) stage 58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM). Differential expression analysis between tissue types at each developmental stage revealed a substantial divergence of ovary and testis transcriptomes starting between NF58 and NF66; transcriptomes continued to diverge through 2WPM. Generally, testis-enriched transcripts were expressed at relatively constant levels, while ovary-enriched transcripts were up-regulated within this developmental period. Functional analyses of differentially expressed transcripts allowed linkages to be made between their putative human orthologues and specific cellular processes associated with differentiating gonad tissues. In ovary tissue, genetic programs direct germ cells through meiosis to the diplotene stage when maternal mRNAs are transcribed and trafficked to oocytes for translation following fertilization. In the testis, gene expression is consistent with connective tissue development, tubule formation, and germ cell support (Leydig and Sertoli cells). This dataset exhibited remarkable consistency with transcript profiles previously described in gonad tissues across species, and emphasizes the universal importance of certain transcripts for germ cell development and preparation of these tissues for reproduction. Four developmental time-points were considered for global expression analysis: NF58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM). Gonad tissues were time-matched and stage-matched, so collection occurred on a single day for each developmental time-point and all animals used were from the same spawn. For the 1WPM and 2WPM time-points, all animals reached NF66 on the same day and were separated from the rest of the spawn until sample collection one and two weeks later respectively. On the day of tissue collection, animals were developmentally staged (Nieuwkoop and Faber, 1994) and euthanized by submersion in a lethal concentration of tricane methanesulfonate ([MS-222], Argent Chemical Laboratories, Redmond, WA, USA) buffered with sodium bicarbonate. Gonad tissues were then excised independently of any other tissues (i.e. “pure” gonad tissue) and transferred to a separate vial for each individual, homogenized in lysis buffer from an RNeasy micro kit (Qiagen Inc., Valencia, CA, USA), and immediately frozen on dry ice until samples could be moved to -80oC storage. Tail or toe tissue was also collected from each individual for genetic sex determination using methods previously described by Olmstead et al. (2010). Once genetic sex was determined for each individual, testes and ovaries were randomly assigned to pools of four individuals (eight gonads per pool) to make a total of five pools of testis tissue and five pools of ovary tissue at each developmental time-point, with the exception of NF58 which had four pools of testis tissue and four pools of ovary tissue (38 total sample pools).

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PolyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf

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