Research Article

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

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Science  20 Sep 2019:
Vol. 365, Issue 6459, eaax1971
DOI: 10.1126/science.aax1971

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Identifying terminal nematode cells

Single-cell RNA sequencing provides the power to identify the developmental trajectory of an organism. However, identifying the temporal lineage of cell development can be difficult without large-scale analyses. Packer et al. sequenced more than 80,000 cells from embryos of the roundworm Caenorhabditis elegans to determine the expression of genes directing the development of terminal cell types. Because all somatic cells in a C. elegans individual have been mapped, the authors are able to connect gene expression with cell lineages over time during development, noting stark transitions in some cases.

Science, this issue p. eaax1971

Structured Abstract


During development, a single-cell zygote undergoes repeated cell divisions to produce an embryo that contains many distinct cell types. This sequence of cell divisions is called the organism’s cell lineage. Each cell in the lineage expresses a different set of genes in various quantities (the cell’s transcriptome), thus directing cells to differentiate into specific cell types over time. Identifying these transcriptome changes and understanding how they regulate cell type specification are fundamental challenges in biology. Advances in methods that assay the mRNA content of single cells [e.g., single-cell RNA sequencing (sc-RNA-seq)] have made it possible to directly measure these gene expression patterns for each cell at a whole-organism scale.


The nematode worm Caenorhabditis elegans has only 558 cells at hatching. Despite its limited cell number, however, C. elegans contains a wide diversity of cell types and a complex anatomy. Its cell lineage is invariant—every individual C. elegans animal is produced by the exact same sequence of cell divisions—and this lineage has been fully mapped. Together, these features make it an ideal animal in which to comprehensively describe the gene expression patterns of each cell and to define the transcriptome dynamics during cell differentiation and development.


We profiled the transcriptomes of 86,024 single cells from C. elegans embryos at developmental stages ranging from gastrulation to terminal cell differentiation. Using computational methods, gene expression patterns from the literature, and gene expression data obtained from three-dimensional (3D) movies of fluorescent reporter lines, we mapped each single-cell transcriptome to its corresponding position in the known C. elegans cell lineage tree. In total, we identified 502 distinct terminal and preterminal cell types, which correspond to 1068 individual branches of the lineage tree. We computed a transcriptional profile for each detected cell type and determined the gene expression differences between mother and daughter cells, and between sister cells, for >200 cell division events in the lineage.

Analyzing these data, we find that:

1) A cell’s lineage history and its transcriptome are transiently correlated. This correlation increases from middle to late gastrulation, then falls substantially as cells adopt their terminal fates.

2) Genes that distinguish sister cells are often first coexpressed in the parent and then selectively retained in one daughter but not the other. This phenomenon, known as “multilineage priming,” is notably prevalent throughout the C. elegans lineage.

3) Most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state, with little or no residual signature of their lineage identity.

4) In many cases, purely computational reconstruction of developmental trajectories from the single-cell transcriptomic data does not accurately reproduce the known cell lineage. Marker genes known to be expressed in specific lineages were critical for correct annotation. This is particularly evident for lineages in which gene expression changes rapidly.


Our dataset defines the succession of gene expression changes associated with almost every cell division in an animal’s embryonic cell lineage. It provides an extensive resource that will guide future investigations of gene regulation and cell fate decisions in C. elegans. It can also serve as a benchmark dataset that will facilitate rigorous evaluation of computational methods for reconstructing cell lineages from sc-RNA-seq data.

UMAP visualization of 86,024 single-cell transcriptomes from C. elegans embryos.

Single-cell transcriptomes were projected into a 3D space by using the uniform manifold approximation and projection (UMAP) algorithm. Each point represents a cell. The projection reconstructs developmental trajectories of C. elegans cell types, spanning from mid-gastrulation (orange and green) to terminal differentiation (blue, purple, and pink).


Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, we find that (i) the correlation between a cell’s lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.

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