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.
K E Y W O R D Scell-intrinsic transcriptional programs, cell-extrinsic signaling environments, evolution of gene expression, EvoDevo, gene co-expression modules, limb development, WGCNA
| INTRODUCTIONRecent advances in single-cell technologies now enable researchers to study the molecular dynamics of pattern formation and evolution at the level of the basic biological unit of life, the individual cell. During development, starting from a single fertilized cell, various progenitor cell populations need to proliferate, differentiate, andfor some of their progeny-undergo controlled cell elimination. These processes require tight coordination, across time and space, to result in proper pattern formation of complex organs. From a cell's perspective, this