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Background  The evolution of novel genes is thought to be a critical component of morphological innovation but few studies have explicitly examined the contribution of novel genes to the evolution of novel tissues. Nematosomes, the free-floating cellular masses that circulate through the body cavity of the sea anemone  Nematostella vectensis , are the defining apomorphy of the genus  Nematostella  and are a useful model for understanding the evolution of novel tissues. Although many hypotheses have been proposed, the function of nematosomes is unknown. To gain insight into their putative function and to test hypotheses about the role of lineage-specific genes in the evolution of novel structures, we have re-examined the cellular and molecular biology of nematosomes.    Results  Using behavioral assays, we demonstrate that nematosomes are capable of immobilizing live brine shrimp ( Artemia salina ) by discharging their abundant cnidocytes. Additionally, the ability of nematosomes to engulf fluorescently labeled bacteria ( E. coli ) reveals the presence of phagocytes in this tissue. Using RNA-Seq, we show that the gene expression profile of nematosomes is distinct from that of the tentacles and the mesenteries (their tissue of origin) and, further, that nematosomes (a  Nematostella -specific tissue) are enriched in  Nematostella -specific genes.    Conclusions  Despite the small number of cell types they contain, nematosomes are distinct among tissues, both functionally and molecularly. We provide the first evidence that nematosomes comprise part of the innate immune system in  N. vectensis , and suggest that this tissue is potentially an important place to look for genes associated with pathogen stress. Finally, we demonstrate that  Nematostella -specific genes comprise a significant proportion of the differentially expressed genes in all three of the tissues we examined and may play an important role in novel cell functions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0683-3) contains supplementary material, which is available to authorized users.

Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis