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Genome Biol. 2018 Aug 24;19(1):124. doi: 10.1186/s13059-018-1498-x.

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

Author information

1
Hospital for Sick Children, Toronto, ON, Canada.
2
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
3
Hospital for Sick Children, Toronto, ON, Canada. bret.pearson@utoronto.ca.
4
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. bret.pearson@utoronto.ca.
5
Ontario Institute for Cancer Research, Toronto, ON, Canada. bret.pearson@utoronto.ca.
6
Hospital for Sick Children, Toronto, ON, Canada. john.parkinson@utoronto.ca.
7
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. john.parkinson@utoronto.ca.
8
Department of Biochemistry, University of Toronto, Toronto, ON, Canada. john.parkinson@utoronto.ca.

Abstract

BACKGROUND:

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 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 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.

CONCLUSIONS:

In 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.

KEYWORDS:

Comparative genomics; Metabolic reconstruction; Metabolism; Schmidtea mediterranea; Single-cell genomics; Tissue regeneration; Transcription factors; Transcriptomics

PMID:
30143032
PMCID:
PMC6109357
DOI:
10.1186/s13059-018-1498-x
[Indexed for MEDLINE]
Free PMC Article

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