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Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

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Item Type:Article
Title:Assessing evolutionary and developmental transcriptome dynamics in homologous cell types
Creators Name:Feregrino, C. and Tschopp, P.
Abstract:BACKGROUND: During 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. RESULTS: Here, 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. CONCLUSIONS: We 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.
Keywords:Cell-Intrinsic Transcriptional Programs, Cell-Extrinsic Signaling Environments, Evolution of Gene Expression, EvoDevo, Gene Co-Expression Modules, Limb Development, WGCNA, Animals, Mice
Source:Developmental Dynamics
Page Range:1472-1489
Date:September 2022
Official Publication:https://doi.org/10.1002/dvdy.384
PubMed:View item in PubMed

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