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Abstract We propose to sequence, assemble and annotate the genome of the clonal cnidarian, Hydractinia. In NUI Galway Hydractinia has been used as a model for stem cell biology and regeneration because, in contrast to mammals, this animal maintains a population of pluripotent stem cells and the ability to regenerate any lost body part as an adult. Through a research project, funded under the SFI Principal Investigator programme, we are currently investigating the molecular mechanisms that control the fate of stem cells in this basal invertebrate. Being small and translucent, Hydractinia offers several advantages for stem cell research by allowing tracking of individual, labeled cells in vivo, hence opening new avenues for stem cell research that are not feasible in mammals. A genome sequence from Hydractinia would significantly augment its value as a model organism for the study of pluripotency and stem cell fate determination. In particular this would enable the investigation of intergenic regulatory regions that control gene expression and the efficient application of new sequence based genomics technologies (e.g. RNA-seq, bisulphite-seq and ChIP-seq) to understand the transcriptional networks and epigenetic modifications that maintain pluripotency and determine lineage commitment.