ArticleDevelopmental dynamics : an official publication of the American Association of Anatomists2022
Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.
Article in Developmental dynamics : an official publication of the American Association of Anatomists, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Library size-stabilized metacells construction enhances co-expression network analysis in single-cell data.PLoS computational biology · 2025Article
- That Stinging Sensation: Modularity and the Origin of the Stinging Cell.Integrative and comparative biology · 2025Review
- Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development.Nature ecology & evolution · 2025Article
- Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome-associated schizophrenia.Nature communications · 2025Article
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- Transient chemical-mediated epigenetic modulation confers unrestricted lineage potential on human primed pluripotent stem cells.Science China. Life sciences · 2025Article
- Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis.Nature communications · 2025Article
- The frequency of CD38Nature communications · 2024Article
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Abstract
backgroundDuring development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built-largely-by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear.
resultsHere, we developed a user-friendly bioinformatics workflow to detect gene co-expression modules and test for their conservation across developmental stages and species boundaries. Using a paradigm of morphological diversification, the tetrapod limb, and single-cell RNA-sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. With mouse limb data as reference, we identified 19 gene co-expression modules with varying tissue or cell type-restricted activities. Testing for co-expression conservation revealed modules with high evolutionary turnover, while others seemed maintained-to different degrees, in module make-up, density or connectivity-over developmental and evolutionary timescales.
conclusionsWe present an approach to identify evolutionary and developmental dynamics in gene co-expression modules during patterning-relevant stages of homologous cell type specification using single-cell RNA-sequencing data.
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