IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43037-0.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43037-0
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-43037-0?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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.
    2. Kyle J. Travaglini & Ahmad N. Nabhan & Lolita Penland & Rahul Sinha & Astrid Gillich & Rene V. Sit & Stephen Chang & Stephanie D. Conley & Yasuo Mori & Jun Seita & Gerald J. Berry & Joseph B. Shrager , 2020. "A molecular cell atlas of the human lung from single-cell RNA sequencing," Nature, Nature, vol. 587(7835), pages 619-625, November.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Qiang Zhang & Sai Ma & Zhengzhi Liu & Bohan Zhu & Zirui Zhou & Gaoshan Li & J. Javier Meana & Javier González-Maeso & Chang Lu, 2023. "Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Yasuaki Uehara & Yusuke Tanaka & Shuyang Zhao & Nikolaos M. Nikolaidis & Lori B. Pitstick & Huixing Wu & Jane J. Yu & Erik Zhang & Yoshihiro Hasegawa & John G. Noel & Jason C. Gardner & Elizabeth J. K, 2023. "Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Lucas F. Loffredo & Anmol Kustagi & Olivia R. Ringham & Fangda Li & Kenia de los Santos-Alexis & Anjali Saqi & Nicholas Arpaia, 2025. "Heparan sulfate regulates amphiregulin programming of tissue reparative lung mesenchymal cells during influenza A virus infection in mice," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    4. Moujtaba Y. Kasmani & Paytsar Topchyan & Ashley K. Brown & Ryan J. Brown & Xiaopeng Wu & Yao Chen & Achia Khatun & Donia Alson & Yue Wu & Robert Burns & Chien-Wei Lin & Matthew R. Kudek & Jie Sun & We, 2023. "A spatial sequencing atlas of age-induced changes in the lung during influenza infection," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    5. Agnieska Brazovskaja & Tomás Gomes & Rene Holtackers & Philipp Wahle & Christiane Körner & Zhisong He & Theresa Schaffer & Julian Connor Eckel & René Hänsel & Malgorzata Santel & Makiko Seimiya & Timm, 2024. "Cell atlas of the regenerating human liver after portal vein embolization," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    6. Nelson Johansen & Hongru Hu & Gerald Quon, 2023. "Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Ava P. Amini & Jesse D. Kirkpatrick & Cathy S. Wang & Alex M. Jaeger & Susan Su & Santiago Naranjo & Qian Zhong & Christina M. Cabana & Tyler Jacks & Sangeeta N. Bhatia, 2022. "Multiscale profiling of protease activity in cancer," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    8. Jimmy Tsz Hang Lee & Sam N. Barnett & Kenny Roberts & Helen Ashwin & Luke Milross & Jae-Won Cho & Alik Huseynov & Benjamin Woodhams & Alexander Aivazidis & Tong Li & Joaquim Majo & Patricia Chaves & M, 2025. "Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    9. Reza Mirzazadeh & Zaneta Andrusivova & Ludvig Larsson & Phillip T. Newton & Leire Alonso Galicia & Xesús M. Abalo & Mahtab Avijgan & Linda Kvastad & Alexandre Denadai-Souza & Nathalie Stakenborg & Ale, 2023. "Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    10. Yuma Takano & Jun Suzuki & Kotaro Nomura & Gento Fujii & Junko Zenkoh & Hitomi Kawai & Yuta Kuze & Yukie Kashima & Satoi Nagasawa & Yuka Nakamura & Motohiro Kojima & Katsuya Tsuchihara & Masahide Seki, 2024. "Spatially resolved gene expression profiling of tumor microenvironment reveals key steps of lung adenocarcinoma development," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    11. Chengdi Wang & Jingwei Li & Jingyao Chen & Zhoufeng Wang & Guonian Zhu & Lujia Song & Jiayang Wu & Changshu Li & Rong Qiu & Xuelan Chen & Li Zhang & Weimin Li, 2025. "Multi-omics analyses reveal biological and clinical insights in recurrent stage I non-small cell lung cancer," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    12. Ze Zhang & Fabao Chen & Zihan Zhang & Luqiang Guo & Tingting Feng & Zhen Fang & Lihui Xin & Yang Yu & Hongyu Hu & Yingbin Liu & Yongning He, 2025. "Structural insights into the in situ assembly of clustered protocadherin γB4," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    13. Seoyeon Lee & Mohammad Naimul Islam & Kaveh Boostanpour & Dvir Aran & Guangchun Jin & Stephanie Christenson & Michael A. Matthay & Walter L. Eckalbar & Daryle J. DePianto & Joseph R. Arron & Liam Mage, 2021. "Molecular programs of fibrotic change in aging human lung," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    14. Andrea Toth & Paranthaman Kannan & John Snowball & Matthew Kofron & Joseph A. Wayman & James P. Bridges & Emily R. Miraldi & Daniel Swarr & William J. Zacharias, 2023. "Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    15. Minhui Chen & Andy Dahl, 2024. "A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    16. Dongpeng Hu & Ichiro Masai, 2025. "Dscamb regulates cone mosaic formation in zebrafish via filopodium-mediated homotypic recognition," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    17. Yan Geng & Lin Li & Jie Yan & Kevin Liu & Aizhen Yang & Lin Zhang & Yingzhi Shen & Han Gao & Xuefeng Wu & Imre Noth & Yong Huang & Junling Liu & Xuemei Fan, 2022. "PEAR1 regulates expansion of activated fibroblasts and deposition of extracellular matrix in pulmonary fibrosis," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    18. Nathanial C. Stevens & Tong Shen & Joshua Martinez & Veneese J. B. Evans & Morgan C. Domanico & Elizabeth K. Neumann & Laura S. Winkle & Oliver Fiehn, 2025. "Resolving multi-image spatial lipidomic responses to inhaled toxicants by machine learning," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    19. Hongru Hu & Gerald Quon, 2024. "scPair: Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    20. Shixuan Liu & Camille Ezran & Michael F. Z. Wang & Zhengda Li & Kyle Awayan & Jonathan Z. Long & Iwijn De Vlaminck & Sheng Wang & Jacques Epelbaum & Christin S. Kuo & Jérémy Terrien & Mark A. Krasnow , 2024. "An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome," Nature Communications, Nature, vol. 15(1), pages 1-27, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43037-0. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.