Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae

What constraints govern the evolution of gene expression patterns across development remains a fundamental question. Single-cell RNA-sequencing can detail these constraints by systematically profiling homologous cells. The conserved invariant embryonic lineage of C. elegans and C. briggsae makes them ideal for comparing cell-type gene expression across evolution. Measuring the spatiotemporal divergence of gene expression across embryogenesis, we find a high level of similarity in gene expression programs between species despite tens of millions of years of evolutionary divergence. Nonetheless, thousands of genes show divergence in their cell-type-specific expression patterns, with enrichment for functions in environmental response and behavior. Neuronal cell types show higher divergence than others, such as the intestine and germline. This work identifies likely constraints on the evolution of developmental gene expression., , # Lineage-resolved analysis of embryonic gene expression evolution in *C. elegans* and *C. briggsae*

Dataset DOI: [10.5061/dryad.1rn8pk15n](10.5061/dryad.1rn8pk15n)

## Description of the data and file structure

### Files and variables

#### File: config.yml

**Description:** Config file needed for VisCello

#### File: clist.rds

**Description:** Cello list of UMAP projections

#### File: cell\_plots.zip

**Description:** Collection of plots describing each progenitor and terminal cell types. Below are the elements in the plots:

1. The relative TPM of every gene in *C. elegans* and *C. briggsae*. Whether a gene is a cell-type marker within that species or both is labeled.
2. A barplot of the cell-type markers from *C. elegans* binned by their WormCat gene category. Ontop is their fold-enrichment and below is their count.
3. The top cell-type markers that are shared between species (black outline), private to *C. elegans* (green), or private to *C. briggsae* (blue). The private marker...,