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Comprehensive single-cell transcriptome lineages of a proto-vertebrate

Author

Listed:
  • Chen Cao

    (Princeton University)

  • Laurence A. Lemaire

    (Princeton University)

  • Wei Wang

    (Stowers Institute for Medical Research)

  • Peter H. Yoon

    (Princeton University)

  • Yoolim A. Choi

    (Princeton University)

  • Lance R. Parsons

    (Princeton University)

  • John C. Matese

    (Princeton University)

  • Wei Wang

    (Princeton University)

  • Michael Levine

    (Princeton University
    Princeton University)

  • Kai Chen

    (Princeton University
    Kunming University of Science and Technology)

Abstract

Ascidian embryos highlight the importance of cell lineages in animal development. As simple proto-vertebrates, they also provide insights into the evolutionary origins of cell types such as cranial placodes and neural crest cells. Here we have determined single-cell transcriptomes for more than 90,000 cells that span the entirety of development—from the onset of gastrulation to swimming tadpoles—in Ciona intestinalis. Owing to the small numbers of cells in ascidian embryos, this represents an average of over 12-fold coverage for every cell at every stage of development. We used single-cell transcriptome trajectories to construct virtual cell-lineage maps and provisional gene networks for 41 neural subtypes that comprise the larval nervous system. We summarize several applications of these datasets, including annotating the synaptome of swimming tadpoles and tracing the evolutionary origin of cell types such as the vertebrate telencephalon.

Suggested Citation

  • Chen Cao & Laurence A. Lemaire & Wei Wang & Peter H. Yoon & Yoolim A. Choi & Lance R. Parsons & John C. Matese & Wei Wang & Michael Levine & Kai Chen, 2019. "Comprehensive single-cell transcriptome lineages of a proto-vertebrate," Nature, Nature, vol. 571(7765), pages 349-354, July.
  • Handle: RePEc:nat:nature:v:571:y:2019:i:7765:d:10.1038_s41586-019-1385-y
    DOI: 10.1038/s41586-019-1385-y
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    Cited by:

    1. Martin Arostegui & R. Wilder Scott & Kerstin Böse & T. Michael Underhill, 2022. "Cellular taxonomy of Hic1+ mesenchymal progenitor derivatives in the limb: from embryo to adult," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    2. Md Tauhidul Islam & Lei Xing, 2023. "Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Jiankai Wei & Wei Zhang & An Jiang & Hongzhe Peng & Quanyong Zhang & Yuting Li & Jianqing Bi & Linting Wang & Penghui Liu & Jing Wang & Yonghang Ge & Liya Zhang & Haiyan Yu & Lei Li & Shi Wang & Liang, 2024. "Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. 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.
    5. Yuan Liao & Lifeng Ma & Qile Guo & Weigao E & Xing Fang & Lei Yang & Fanwei Ruan & Jingjing Wang & Peijing Zhang & Zhongyi Sun & Haide Chen & Zhongliang Lin & Xueyi Wang & Xinru Wang & Huiyu Sun & Xiu, 2022. "Cell landscape of larval and adult Xenopus laevis at single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Zhijun Dong & Fanghan Wang & Yali Liu & Yongxue Li & Haiyan Yu & Saijun Peng & Tingting Sun & Meng Qu & Ke Sun & Lei Wang & Yuanqing Ma & Kai Chen & Jianmin Zhao & Qiang Lin, 2024. "Genomic and single-cell analyses reveal genetic signatures of swimming pattern and diapause strategy in jellyfish," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Toshio Sekiguchi & Hiroshi Akitaya & Satoshi Nakayama & Takashi Yazawa & Michio Ogasawara & Nobuo Suzuki & Kazuichi Hayakawa & Shuichi Wada, 2020. "Effect of Polycyclic Aromatic Hydrocarbons on Development of the Ascidian Ciona intestinalis Type A," IJERPH, MDPI, vol. 17(4), pages 1-11, February.
    8. Xavier Grau-Bové & Lucie Subirana & Lydvina Meister & Anaël Soubigou & Ana Neto & Anamaria Elek & Silvia Naranjo & Oscar Fornas & Jose Luis Gomez-Skarmeta & Juan J. Tena & Manuel Irimia & Stéphanie Be, 2024. "An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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