The head-regeneration transcriptome of the planarian Schmidtea mediterraneaReport as inadecuate

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Genome Biology

, 12:R76

First Online: 16 August 2011Received: 25 March 2011Revised: 13 July 2011Accepted: 16 August 2011


BackgroundPlanarian 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.

ResultsTo 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.

ConclusionsTranscriptome 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.

Abbreviationsbpbase pair

CNScentral nervous system

djDugesia japonica

dsRNAdouble-stranded RNA

EGRearly growth response gene family

ESTexpressed sequence tag

GOgene ontology


PBSTphosphate-buffered saline with Tween 20

PCRpolymerase chain reaction

qRT-PCRquantitative reverse transcriptase PCR

RNAiRNA interference

TNFRtumor necrosis factor receptor

TRAFtumor necrosis factor receptor associated protein.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2011-12-8-r76 contains supplementary material, which is available to authorized users.

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Author: Thomas Sandmann - Matthias C Vogg - Suthira Owlarn - Michael Boutros - Kerstin Bartscherer


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