Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary

Abstract

Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function and the transcriptome profiles will provide a valuable resource for future studies.

Data availability

The raw and processed data reported in this paper are archived at NCBI GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE191137) and in an interactively browsable forms at the Broad Institute Single-Cell Portal (https://singlecell.broadinstitute.org/single_cell/study/SCP928/40dpf-ovary-all-cells). Analysis code and objects are archived at github (https://github.com/yulongliu68/zeb_ov_ssRNAseq). Gene expression tables for the cell clusters identified are archived at Dryad: (https://datadryad.org/stash/share/CEd0Zs4oZKdinTWeJPKbWYjBq6hYq4QhVacQcFjf37E).

The following data sets were generated

Article and author information

Author details

  1. Yulong Liu

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Michelle E Kassack

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Matthew E McFaul

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Lana N Christensen

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Stefan Siebert

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Sydney R Wyatt

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Caramai N Kamei

    Mount Desert Island Biological Laboratory, Bar Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Samuel Horst

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Nayeli Arroyo

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Iain A Drummond

    Mount Desert Island Biological Laboratory, Bar Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Celina E Juliano

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4222-0987
  12. Bruce W Draper

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    For correspondence
    bwdraper@ucdavis.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4397-7749

Funding

National Institutes of Health (R01 HD-081551)

  • Yulong Liu
  • Matthew E McFaul
  • Lana N Christensen
  • Bruce W Draper

National Science Foundation (IOS-1456737)

  • Michelle E Kassack
  • Lana N Christensen
  • Bruce W Draper

National Institutes of Health (T32 training grant ES-0070599)

  • Michelle E Kassack

National Institutes of Health (T32 training grant GM-007377)

  • Matthew E McFaul
  • Sydney R Wyatt

National Science Foundation (GRFP 2036201)

  • Sydney R Wyatt

National Institutes of Health (R35 GM133689)

  • Stefan Siebert
  • Celina E Juliano

National Institutes of Health (R01 DK126021)

  • Iain A Drummond

National Institutes of Health (R01)

  • Caramai N Kamei
  • Iain A Drummond

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (#20200 and #20201) of the University of California, Davis.

Reviewing Editor

  1. John Postlethwait

Version history

  1. Preprint posted: December 1, 2021 (view preprint)
  2. Received: December 1, 2021
  3. Accepted: May 18, 2022
  4. Accepted Manuscript published: May 19, 2022 (version 1)
  5. Version of Record published: June 13, 2022 (version 2)

Copyright

© 2022, Liu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Yulong Liu
  2. Michelle E Kassack
  3. Matthew E McFaul
  4. Lana N Christensen
  5. Stefan Siebert
  6. Sydney R Wyatt
  7. Caramai N Kamei
  8. Samuel Horst
  9. Nayeli Arroyo
  10. Iain A Drummond
  11. Celina E Juliano
  12. Bruce W Draper
(2022)
Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary
eLife 11:e76014.
https://doi.org/10.7554/eLife.76014

Share this article

https://doi.org/10.7554/eLife.76014

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