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Cited by 44Single-cell and spatial transcriptomicsZebrafish Biomedical Research ApplicationsDevelopmental Biology and Gene Regulation

A single-cell transcriptome atlas of the maturing zebrafish telencephalon

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Pandey, Shristi, Moyer, Anna J., Thyme, Summer B.·2023·Genome Research
DOI 10.1101/gr.277278.122PMC PMC10234298
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Abstract

The zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon, we delineated nine main neuronal cell types in the pallium and eight in the subpallium and nominated novel marker genes. Comparing zebrafish and mouse neuronal cell types revealed both conserved and absent types and marker genes. Mapping of cell types onto a spatial larval reference atlas created a resource for anatomical and functional studies. Using this multiage approach, we discovered that although most neuronal subtypes are established early in the 6-dpf fish, some emerge or expand in number later in development. Analyzing the samples from each age separately revealed further complexity in the data, including several cell types that expand substantially in the adult forebrain and do not form clusters at the larval stages. Together, our work provides a comprehensive transcriptional analysis of the cell types in the zebrafish telencephalon and a resource for dissecting its development and function.

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Cited by

Sorted by citations

Authors
Pandey, S., Moyer, A. J., & Thyme, S. B.
Affiliations
  • Harvard University (US)
  • University of Alabama at Birmingham (US)
Corresponding author
  • Pandey, Shristi
  • Thyme, Summer B.
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2023-04
Volume
33
Issue
4
Pages
658-671
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.277278.122
PMC
PMC10234298
OpenAlex
W4366249037
Cited by
44
References
2
Citations by year
2026: 19 · 2025: 11 · 2024: 8 · 2023: 6
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health (DP1HD094764, R00MH110603)
  • Allen Discovery Center
  • McKnight Foundation
  • Klingenstein-Simons (T32HG008961)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
forebrain development, neuronal cell types, pallium, subpallium, cell type markers, larval to adult transition, single-cell transcriptomics
MeSH terms
Animals, Neurons, Telencephalon, Zebrafish, Zebrafish Proteins, Mice, Transcriptome

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