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A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines

Author

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  • Komal Kumar Bollepogu Raja

    (Baylor College of Medicine, One Baylor Plaza)

  • Kelvin Yeung

    (Baylor College of Medicine, One Baylor Plaza)

  • Yoon-Kyung Shim

    (Baylor College of Medicine, One Baylor Plaza)

  • Yumei Li

    (Baylor College of Medicine, One Baylor Plaza
    Baylor College of Medicine, One Baylor Plaza)

  • Rui Chen

    (Baylor College of Medicine, One Baylor Plaza
    Baylor College of Medicine, One Baylor Plaza)

  • Graeme Mardon

    (Baylor College of Medicine, One Baylor Plaza
    Baylor College of Medicine, One Baylor Plaza)

Abstract

The Drosophila eye is a powerful model system to study the dynamics of cell differentiation, cell state transitions, cell maturation, and pattern formation. However, a high-resolution single cell genomics resource that accurately profiles all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as strands of cells that represent their dynamic developmental timelines. As photoreceptor subtypes mature, they appear to assume a common transcriptomic profile that is dominated by genes involved in axon function. We identify cell type maturation genes, enhancers, and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that the chromatin accessibility between cones and photoreceptors is distinct. These single cell genomics atlases will greatly enhance the power of the Drosophila eye as a model system.

Suggested Citation

  • Komal Kumar Bollepogu Raja & Kelvin Yeung & Yoon-Kyung Shim & Yumei Li & Rui Chen & Graeme Mardon, 2023. "A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43037-0
    DOI: 10.1038/s41467-023-43037-0
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    References listed on IDEAS

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    1. Manolis Fanto & Marek Mlodzik, 1999. "Asymmetric Notch activation specifies photoreceptors R3 and R4 and planar polarity in the Drosophila eye," Nature, Nature, vol. 397(6719), pages 523-526, February.
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    3. Michael T. D. Cooper & Sarah J. Bray, 1999. "Frizzled regulation of Notch signalling polarizes cell fate in the Drosophila eye," Nature, Nature, vol. 397(6719), pages 526-530, February.
    4. S. Sean Millard & John J. Flanagan & Kartik S. Pappu & Wei Wu & S. Lawrence Zipursky, 2007. "Dscam2 mediates axonal tiling in the Drosophila visual system," Nature, Nature, vol. 447(7145), pages 720-724, June.
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