Fig. 5.

Bulk RNA-seq suggests that the formation of differentiated tissues occurs only after the dimple stage in Hofstenia miamia. (A) PCA plot of all samples shows that the early-cleavage and gastrula stages are transcriptionally distinct from all other stages. Colors represent samples from the same developmental stage. (B) Heatmap of the mean TPM values across three biological replicates per developmental stage of genes that are significantly differentially expressed during development (likelihood ratio test). Columns represent developmental stages, whereas rows represent genes. The dashed lines demarcate gene clusters generated from hierarchical clustering that have similar expression profiles across development. Each cluster identity is labeled on the left of the heatmap. Representative GO terms associated with each cluster are listed on the right of the heatmap. (C) Mean TPM values for known differentiated tissue marker genes. All markers shown have expression levels that increase only after the dimple stage. The legend for the x-axis for all graphs is shown at the bottom.