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The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Thomas Sandmann12*, Matthias C Vogg3, Suthira Owlarn3, Michael Boutros14 and Kerstin Bartscherer3*

Author Affiliations

1 Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany

2 CellNetworks Cluster of Excellence, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany

3 Max Planck Research Group Stem Cells and Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, 48149 Münster, Germany

4 Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany

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Genome Biology 2011, 12:R76  doi:10.1186/gb-2011-12-8-r76

Published: 16 August 2011



Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown.


To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning.


Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.