An ancient split of germline and somatic stem cell lineages in Hydra

<jats:title>Abstract</jats:title> <jats:p> In many animals, germ cell segregation occurs during early embryogenesis to protect the genome, but its origin in basal metazoans is controversial. Here, we show in the freshwater polyp <jats:italic>Hydra</jats:italic> by clonal analysis and transgenic animals that interstitial stem cells comprise two separate stem cell populations, i.e., germline and multipotent somatic stem cells. We isolated genetically labelled stem cells for a global transcriptome study and discovered a broad set of germline-specific/enriched genes including <jats:italic>Prdm9, Pax5, Dmrt1</jats:italic> . In an alternative splicing analysis, we identified many genes with germline-specific isoforms; among them, male-specific isoforms of <jats:italic>Dmrt1</jats:italic> and <jats:italic>Snf5</jats:italic> . The somatic interstitial stem cell lineage was characterized by numerous neuronal control genes like <jats:italic>Neurog</jats:italic> . But all stem cells in <jats:italic>Hydra</jats:italic> also share a core of stemness genes that has its roots in unicellular eukaryotes. This suggests an evolutionary scenario in which, at the emergence of animal multicellularity, there was an early split into a stable germline and different somatic stem cell lineages. </jats:p>