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Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis
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Functional and evolutionary insights from the Ciona notochord transcriptome.

Wendy M Reeves1, Yuye Wu1, Matthew J Harder1

  • 1Division of Biology, Kansas State University, Manhattan, KS 66506, USA.

Development (Cambridge, England)
|September 21, 2017
PubMed
Summary

This study defines the complete set of genes in the Ciona notochord, revealing conserved genes from tunicates to vertebrates. It also shows Brachyury is not a master regulator of notochord development.

Keywords:
CionaNotochordTranscriptome

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Area of Science:

  • Developmental Biology
  • Genomics
  • Evolutionary Biology

Background:

  • The ascidian Ciona notochord, a simple 40-cell structure, is a key model for studying organogenesis.
  • Understanding notochord development is crucial for insights into embryonic development and evolution.

Purpose of the Study:

  • To create a comprehensive transcriptome of the Ciona notochord.
  • To identify genes involved in notochord development and conserved across vertebrates.
  • To investigate the role of the transcription factor Brachyury in notochord development.

Main Methods:

  • RNA sequencing (RNAseq) on flow-sorted Ciona notochord cells across multiple developmental stages.
  • Validation of gene expression using in situ hybridization.
  • Comparative analysis of Ciona notochord genes with vertebrate notochord expression data.

Main Results:

  • Identified 1364 genes with enriched expression in the Ciona notochord.
  • Validated genes are enriched for functions in extracellular matrix, cell adhesion, and cytoskeleton.
  • Found 112 Ciona notochord genes with conserved expression in vertebrate notochords, exceeding chance predictions.
  • Demonstrated modest overlap between notochord-enriched genes and those upregulated by Brachyury, challenging its role as a master regulator.

Conclusions:

  • The comprehensive Ciona notochord transcriptome provides a foundation for systems-level studies of notochord gene regulation and morphogenesis.
  • Conserved notochord genes offer valuable tools for studying notochord evolution from tunicates to vertebrates.
  • Brachyury's role in notochord development may be more nuanced than previously thought, not acting as a sole master regulator.