SRP121652 PRJNA415947 GSE106219 FOX and ETS family transcription factors regulate the pigment cell lineage in planarians Many pigment cells acquire unique structural properties and gene expression profiles during animal development. The underlying differentiation pathways have been well characterized in cells formed during embryogenesis, such as the neural crest-derived melanocyte. However, much less is known about the developmental origins of pigment cells produced in adult organisms during tissue homeostasis and repair. Here we report a lineage analysis of ommochrome- and porphyrin-producing cells in the brown, freshwater planarian Schmidtea mediterranea. Using an RNA-sequencing approach, we identified two classes of markers expressed in sequential fashion when new pigment cells are generated during regeneration or in response to pigment cell ablation. We also report roles for FOXF-1 and ETS-1 transcription factors, as well as an FGF Receptor-like molecule, in the specification and maintenance of this cell type. Together, our results provide the first insight into mechanisms of adult pigment cell development in the strikingly colorful Platyhelminthes phylum. Overall design: RNA deep sequencing (RNAseq) was performed on wildtype (WT) animals as well as fully depigmented animals (8 days of depigmentation by light exposure) and partially repigmented animals (1, 2 and 8 days of repigmentation in the dark on starved animals). Experiments were performed in biological-triplicate but mixed in equal amounts prior to sequencing, sequenced to a depth of ~40 million reads per sample, and multiplexed on an Illumina HiSeq2500 with 50 base pair, single-end reads. 75 genes of interest were identified based on high 8 day WT:depigmented fold change. Raw scRNAseq data (including stem cells, neurons, gut, epithelial, muscle and parapharyngeal cells) were obtained from the NCBI Sequence Read Archive (SRA:PRJNA276084) and the NCBI Gene Expression Omnibus (GEO:GSE79866) (Molinaro and Pearson, 2016; Wurtzel et al., 2015). Reads were aligned to the SmedASXL transcriptome assembly under NCBI BioProject PRJNA215411 using bowtie2 (Langmead and Salzberg, 2012) with 15 bp 3' trimming. GSE106219 pubmed 29158443