Abstract
The planarian Schmidtea mediterranea is a powerful model organism for studying stem cell biology due to its extraordinary regenerative ability mediated by neoblasts, a population of adult somatic stem cells. Elucidation of the S. mediterranea transcriptome and the dynamics of transcript expression will increase our understanding of the gene regulatory programs that regulate stem cell function and differentiation. Here, we have used RNA-Seq to characterize the S. mediterranea transcriptome in sexual and asexual animals and in purified neoblast and differentiated cell populations. Our analysis identified many uncharacterized genes, transcripts, and alternatively spliced isoforms that are differentially expressed in a strain or cell type-specific manner. Transcriptome profiling of purified neoblasts and differentiated cells identified neoblast-enriched transcripts, many of which likely play important roles in regeneration and stem cell function. Strikingly, many of the neoblast-enriched genes are orthologs of genes whose expression is enriched in human embryonic stem cells, suggesting that a core set of genes that regulate stem cell function are conserved across metazoan species.
Highlights
The freshwater planarian Schmidtea mediterranea has emerged as an important model organism for studying stem cell biology and regeneration, because of its’ ability to completely regenerate following injury [1,2]
RNA-Seq Based de novo Transcript Assembly To characterize the S. mediterranea transcriptome and to identify genes and mRNA isoforms that are expressed in a strain- and neoblast-specific manner, we performed single and paired-end RNA-Seq of mRNA isolated from sexual and asexual animals that were either non-irradiated or irradiated (GEO accession: GSE34326)
Our analysis revealed that 13% (455/3,429) of the genes predominantly expressed in X1 neoblasts and 8.7% (397/4,525) of the genes predominantly expressed in differentiated Xins cells have human orthologs
Summary
The freshwater planarian Schmidtea mediterranea has emerged as an important model organism for studying stem cell biology and regeneration, because of its’ ability to completely regenerate following injury [1,2]. S. mediterranea is a non-parasitic flatworm in the phylum Platyhelminthes, a clade of metazoans largely unexplored using genomic approaches. Recent analyses have more thoroughly interrogated the S. mediterranea transcriptome using RNA-Seq and identified a significantly larger fraction of transcribed sequences in the genome [6,7,8]. None of these studies examined the dynamics of gene expression in different strains or in different cell types
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