Cell type transcriptome atlas for the planarian Schmidtea mediterranea

Abstract

The transcriptome of a cell dictates its unique cell type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and represents a powerful approach to metazoan biology.

foxF-1 Controls Specification of Non-body Wall Muscle and Phagocytic Cells in Planarians

“…FISH for mp-1 and mhc-2 showed that all DVM co-expressed both markers; however, some cells around intestinal branches expressed only mp-1 (Figure 1E; Figure S1E,F). Moreover, the recently described marker dd_12771(PTPRD) [13] had enriched expression in cluster 6 (Figure 1F), and FISH showed that dd_12771(PTPRD) + cells also expressed mp-1 but not mhc-2, indicating that cluster 6 represents IM (Figure 1F; Figure S1E,F). Finally, pharynx muscle marker (dd_8356) expression [13, 15] was restricted to cluster 7, which was therefore considered pharynx muscle (Figure 1C).…”

“…Moreover, the recently described marker dd_12771(PTPRD) [13] had enriched expression in cluster 6 (Figure 1F), and FISH showed that dd_12771(PTPRD) + cells also expressed mp-1 but not mhc-2, indicating that cluster 6 represents IM (Figure 1F; Figure S1E,F). Finally, pharynx muscle marker (dd_8356) expression [13, 15] was restricted to cluster 7, which was therefore considered pharynx muscle (Figure 1C). In summary, we identified transcriptomes for four main classes of muscle: BWM (including longitudinal and circular fibers), DVM, IM, and pharynx muscle.…”

“…240 muscle cells were analysed using Seurat [12] and data were visualized using t-stochastic neighbour embedding (t-SNE; Methods). We identified seven muscle cell clusters (Figure 1B), which expressed well-characterized muscle markers (Figure S1C; [1, 11, 13]). Differential expression analysis between clusters identified cluster-enriched markers (Table S2).…”

“…Gene expression analysis by Smart-Seq SCS and fluorescence in situ hybridization (FISH) showed that previously described muscle markers [3, 11, 13] were expressed in specific muscle cell clusters. For example, body wall muscle-1 (dd_5321, bwm-1) (Figure S1E; [11]) was expressed in all BWM cells (by FISH) and its expression was highly enriched in clusters 1, 2, 3, and 4 but excluded from clusters 5, 6, and 7 (Figure 1C).…”

“…To validate these findings, we performed a clustering analysis of muscle cells from a recently described Drop-Seq SCS (in short, Drop-Seq) dataset [13], generating 13 cell clusters (Figure S2A,B; Data S1). Similar to the Smart-Seq SCS analysis described above, cells with high smedwi-1 expression levels were clustered together with cells with low or no smedwi-1 expression but higher expression levels of differentiated markers, suggesting these cells represent transient stages of muscle differentiation (Figure S2C).…”