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Background  Germ cells are specified during early development and are responsible for generating gametes in the adult. After germ cells are specified, they typically migrate to a particular niche in the organism where they reside for the remainder of its lifetime. For some model organisms, the specification and migration of germ cells have been extensively studied, but how these events occur in animals that reproduce both sexually and asexually is not well understood.    Results  We have identified a novel TGF-β family member in  Botryllus schlosseri ,  tgfβ - f , and found that it is expressed by follicle cell progenitors and the differentiated follicle and support cells surrounding the maturing gametes. Using the expression of  tgfβ - f  and the germ cell marker  vasa , we have found that nearly all germ cells in  Botryllus  are associated with  tgfβ - f -expressing follicle progenitors in clusters consisting solely of those two cell types. These clusters were mostly small, consisting of ten or fewer cells, and generally contained between a 2:1 and 1:1 ratio of follicle progenitors to germ cells. Clusters of germ and follicle progenitor cells were primarily localized to niches in the primary and secondary buds, but could also be found in other locations including the vasculature. We analyzed the location of germ cell clusters throughout the asexual life cycle of  Botryllus  and found that at the stage when germ cells are first detected in the secondary bud niche, a dramatic change in the size and location of germ/follicle cell clusters also occurred.    Conclusions  Our findings suggest that germ/follicle cell clusters have predictable migratory patterns during the weekly asexual developmental cycle in  Botryllus . An increased number of small clusters and the presence of clusters in the vasculature coinciding with the appearance of clusters in the secondary bud suggest that fragmentation of clusters and the migration of smaller clusters through the vasculature may be an important aspect of  Botryllus  reproductive biology, ensuring the transmission of the germline to subsequent asexual generations.    Electronic supplementary material  The online version of this article (doi:10.1186/s13227-016-0047-5) contains supplementary material, which is available to authorized users.

Temporally and spatially dynamic germ cell niches in Botryllus schlosseri revealed by expression of a TGF-beta family ligand and vasa