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Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.

Christian Feregrino1,2, Patrick Tschopp1

  • 1DUW Zoology, University of Basel, Basel, Switzerland.

Developmental Dynamics : an Official Publication of the American Association of Anatomists
|June 11, 2021
PubMed
Summary
This summary is machine-generated.

Investigating gene co-expression modules in homologous cell types reveals evolutionary changes in transcriptional programs. This study analyzes tetrapod limb development in chickens and mice to understand cell type specification across species.

Keywords:
EvoDevoWGCNAcell-extrinsic signaling environmentscell-intrinsic transcriptional programsevolution of gene expressiongene co-expression moduleslimb development

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Area of Science:

  • Developmental Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Complex organ patterns arise from precise cell type specification during development.
  • Morphological diversification occurs over evolutionary timescales.
  • Homologous structures are generally formed by homologous cell types, but their transcriptional programs may not be conserved.

Purpose of the Study:

  • To develop a bioinformatics workflow for detecting and testing gene co-expression module conservation across species and developmental stages.
  • To assess transcriptional dynamics of homologous cell types during embryonic patterning using single-cell RNA sequencing (scRNA-seq) data.
  • To investigate evolutionary and developmental dynamics in gene co-expression modules during homologous cell type specification.

Main Methods:

  • Developed a user-friendly bioinformatics workflow.
  • Utilized single-cell RNA sequencing (scRNA-seq) data from chicken and mouse embryonic limbs.
  • Analyzed gene co-expression modules and their conservation across species and developmental stages.

Main Results:

  • Identified 19 gene co-expression modules with cell type-specific activities in the tetrapod limb.
  • Found significant evolutionary turnover in some gene co-expression modules.
  • Observed varying degrees of module conservation in composition, density, and connectivity across evolutionary and developmental timescales.

Conclusions:

  • The developed approach identifies evolutionary and developmental dynamics in gene co-expression modules.
  • Homologous cell types exhibit both conserved and divergent transcriptional specification programs.
  • This work provides insights into the molecular basis of morphological diversification.