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The regeneration-capable flatworm  Macrostomum lignano  is a powerful model organism to study the biology of stem cells in vivo. As a flatworm amenable to transgenesis, it complements the historically used planarian flatworm models, such as  Schmidtea mediterranea . However, information on the transcriptome and markers of stem cells in  M. lignano  is limited. We generated a de novo transcriptome assembly and performed the first comprehensive characterization of gene expression in the proliferating cells of  M. lignano , represented by somatic stem cells, called neoblasts, and germline cells. Knockdown of a selected set of neoblast genes, including  Mlig-ddx39 ,  Mlig-rrm1 ,  Mlig-rpa3 ,  Mlig-cdk1 , and  Mlig-h2a , confirmed their crucial role for the functionality of somatic neoblasts during homeostasis and regeneration. The generated  M. lignano  transcriptome assembly and gene expression signatures of somatic neoblasts and germline cells will be a valuable resource for future molecular studies in  M. lignano .

Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano