Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution

Mitsuru J. Nakamura, Jun Terai, Reiko Okubo, Kohji Hotta, Kotaro Oka

Research output: Contribution to journalArticlepeer-review

36 Citations (Scopus)


During embryogenesis, chordates pass through a tailbud stage in which the larval tail is formed. Since acquisition of a tadpole-like tail during tailbud stage is one of the key events in the evolution of chordates, understanding the anatomy of the tailbud stage chordate embryo is of special interest. In this study, to understand comprehensively the anatomy of the tailbud embryo at single-cell-level, real microscopic image stacks of the tailbud embryo in Ciona intestinalis were reconstructed into a 3D computer model. This comprehensive 3D model of the ascidian tailbud embryo was based on real images of confocal laser scanning microscope (CLSM) and therefore, cell shape, location and cell arrangement reflect real geometries of the tailbud embryo. We found that the tailbud embryo consists of 1579 cells, including 836 epidermal cells, 228 cells in the central nervous system, 218 mesenchymal cells, four trunk ventral cells, two B/B*8.11 cells, 36 muscle cells, 40 notochord cells, four primordial germ cells, and 199 endodermal cells. Moreover, we identified for the first time two populations of previously undefined cells (a total of 12 cells) in Ciona: one located in the lateral trunk and the other located under the tail dorsal epidermis. This information provides a first step for understanding how the body plan of the chordate tailbud embryo formed and evolved.

Original languageEnglish
Pages (from-to)274-284
Number of pages11
JournalDevelopmental Biology
Issue number2
Publication statusPublished - 2012 Dec 15


  • Anatomy
  • Cell lineage
  • Chordate evolution
  • Interactive 3D visualization
  • Segmentation
  • Tunicate

ASJC Scopus subject areas

  • Molecular Biology
  • Developmental Biology
  • Cell Biology


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