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Background  Gonad differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. The colonial ascidian,  Botryllus schlosseri  is a chordate model organism which offers two unique traits that can be utilized to characterize the genes underlying germline development: a colonial life history and variable fertility. These properties allow individual genotypes to be isolated at different stages of fertility and gene expression can be characterized comprehensively.    Results  Here we characterized the transcriptome of both fertile and infertile colonies throughout blastogenesis (asexual development) using differential expression analysis. We identified genes (as few as 7 and as many as 647) regulating fertility in  Botryllus  at each stage of blastogenesis. Several of these genes appear to drive gonad maturation, as they are expressed by follicle cells surrounding both testis and oocyte precursors. Spatial and temporal expression of differentially expressed genes was analyzed by  in situ  hybridization, confirming expression in developing gonads.    Conclusion  We have identified several genes expressed in developing and mature gonads in  B. schlosseri . Analysis of genes upregulated in fertile animals suggests a high level of conservation of the mechanisms regulating fertility between basal chordates and vertebrates.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-1183) contains supplementary material, which is available to authorized users.

Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility