GSE115280
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identifies major cell types and pathway conservation
Background:  In the Lophotrochozoan superphylum, few organisms have the capacity for rapid  testing of gene function and single-cell transcriptomics as the freshwater planarian.  The species Schmidtea mediterranea in particular has become a powerful model to  study adult stem cell biology and mechanisms of regeneration. Despite this,  systematic attempts to define gene complements and their annotations are lacking,  restricting comparative analyses that detail the conservation of biochemical pathways  and identify lineage-specific innovations.  Results:  In this study we compare several transcriptomes and define a robust set of 35,232  transcripts. From this, we perform systematic gene annotations and undertake a  genome-scale metabolic reconstruction for S. mediterranea. Cross-species  comparisons of gene content identify both conserved, lineage-specific, and expanded  gene families, which may contribute to the regenerative properties of planarians. In  particular, we find that TRAF and cadherin gene families have been greatly expanded  in planarians. We further provide a single-cell RNA-sequencing analysis of 2000 cells,  revealing both known and novel cell-types defined by unique signatures of gene  expression. Amongst these were a novel mesenchymal cell population as well as a cell  type involved in eye regeneration. Integration of our metabolic reconstruction further  reveals the extent to which a given cell types have adapted energy and nucleotide  biosynthetic pathways to support their specialized roles.  Conclusions:  In general, S. mediterranea displays a high level of gene and pathways conservation  with other model systems, rendering it as a viable model to study the roles of these  pathways in stem cell biology and regeneration. Overall design: Wildtype animals were mechanically dissociated in Calcium-magnesium free media (CMF) with 1% BSA and stained with calcein to label live cells. Calcein-positive cells were collected by FACS. Cells were barcoded and cDNA libraries were prepared in nanoliter droplets using Drop-seq. The cDNA library pool was sequenced to a total depth of 480 million paired-end reads on an Illumina NextSeq500.