Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Issue 9 (16th June 2021)

• Record Type: Journal Article
• Authors: Feregrino, Christian; Tschopp, Patrick
• Other Names: Sears Karen E. guestEditor.; Gros Jerome guestEditor.; Davey Megan guestEditor.
• Is Part Of: Developmental dynamics. Volume 251:Issue 9(2022)
• Page Start: 1472
• Page End: 1489
• Publication Date: 2021-06-16
• Subjects: cell‐intrinsic transcriptional programs -- cell‐extrinsic signaling environments -- evolution of gene expression -- EvoDevo -- gene co‐expression modules -- limb development -- WGCNA; Morphogenesis -- Periodicals; Anatomy -- Periodicals; Anatomie -- Périodiques; Biologie du développement -- Périodiques; 571.833
• DOI: 10.1002/dvdy.384
• Languages: English
• ISSNs: 1058-8388

Abstract

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. Key Findings: 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.