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Background  The  Sox  genes are important regulators of animal development belonging to the HMG domain-containing class of transcription factors. Studies in bilaterian models have notably highlighted their pivotal role in controlling progression along cell lineages, various  Sox  family members being involved at one side or the other of the critical balance between self-renewing stem cells/proliferating progenitors, and cells undergoing differentiation.    Results  We have investigated the expression of 10  Sox  genes in the cnidarian  Clytia hemisphaerica . Our phylogenetic analyses allocated most of these  Clytia  genes to previously-identified Sox groups: SoxB ( CheSox2, CheSox3, CheSox10, CheSox13, CheSox14 ), SoxC ( CheSox12 ), SoxE ( CheSox1, CheSox5 ) and SoxF ( CheSox11 ), one gene ( CheSox15 ) remaining unclassified. In the planula larva and in the medusa, the  SoxF  orthologue was expressed throughout the endoderm. The other genes were expressed either in stem cells/undifferentiated progenitors, or in differentiating (-ed) cells with a neuro-sensory identity (nematocytes or neurons). In addition, most of them were expressed in the female germline, with their maternal transcripts either localised to the animal region of the egg, or homogeneously distributed.    Conclusions  Comparison with other cnidarians, ctenophores and bilaterians suggest ancient evolutionary conservation of some aspects of gene expression/function at the  Sox  family level: (i) many  Sox  genes are expressed in stem cells and/or undifferentiated progenitors; (ii) other genes, or the same under different contexts, are associated with neuro-sensory cell differentiation; (iii)  Sox  genes are commonly expressed in the germline; (iv)  SoxF  group genes are associated with endodermal derivatives. Strikingly, total lack of correlation between a given  Sox  orthology group and expression/function in stem cells/progenitors  vs . in differentiating cells implies that  Sox  genes can easily switch from one side to the other of the balance between these fundamental cellular states in the course of evolution.

Multiple Sox genes are expressed in stem cells or in differentiating neuro-sensory cells in the hydrozoan Clytia hemisphaerica