Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

Lakshmipuram Seshadri Swapna,John Parkinson,Bret J Pearson,Alyssa M Molinaro,Nicole Lindsay-Mosher

doi:10.1186/s13059-018-1498-x

Lakshmipuram Seshadri Swapna, John Parkinson + Show 3 more

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https://doi.org/10.1186/s13059-018-1498-x

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Abstract

BackgroundIn the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying 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.ResultsIn this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has 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. Among these are 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 given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles.ConclusionsIn general, S. mediterranea displays a high level of gene and pathway conservation compared with other model systems, rendering it a viable model to study the roles of these pathways in stem cell biology and regeneration.

Highlights

In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria
A definitive transcriptome for S. mediterranea A definitive transcriptome of S. mediterranea was generated by integrating the RNA sequencing (RNA-seq) reads generated from five separate experiments and cell purifications [18, 31,32,33] (National Center for Biotechnology Information [NCBI] Bioproject PRJNA215411)
Protein-coding transcripts are identified on the basis of sequence similarity to known transcripts or proteins, as well as the presence of predicted protein domains with reference to the following databases: UniProt [34], MitoCarta [35], InterPro [36], Core Eukaryotic Genes Mapping Approach (CEGMA) [37], Benchmarking Universal Single-Copy Orthologs (BUSCO) [38], and ESTs of other known platyhelminth transcriptomes deposited in the expressed sequence tag (EST) database of the NCBI: Biomphalaria glabrata, Clonorchis sinensis, Crassostrea gigas, Dugesia japonica, Dugesia ryukyuensis, Echinococcus granulosus, Echinococcus multilocularis, Helobdella robusta, Hirudo medicinalis, Hymenolepis microstoma, Macrostomum lignano, Mytilus californianus, Opisthorchis viverrini, Schistosoma japonicum, Schistosoma mansoni, Taenia solium

Summary

Introduction

In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite significant resources put forth to develop S. mediterranea as a model in the lab, systematic genome-scale investigations of gene function and conservation are lacking. Placing gene function in an evolutionary context is critical to inform on the conservation of pathways related to stem cell biology and regeneration, and because planarians represent a key member of the otherwise neglected superphylum Lophotrochozoa/Spiralia (subsequently referred to as Lophotrochozoa), and they can further be used to model closely related parasitic flatworm species (e.g., flukes and tapeworms), which infect an estimated hundreds of millions worldwide [8]

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