A wave of hematopoietic stem cell-derived T/ILC-restricted progenitors initiates thymopoiesis and shapes the embryonic thymus architecture.

Multiple waves of hematopoietic progenitors with distinct lineage potentials are differentially regulated in time and space. The site of origin and the cellular outputs of the first wave of thymic seeding progenitors remain unclear. Here we show that these progenitors are T/ILC restricted and unique in generating lymphoid tissue inducer cells, in addition to embryonic-derived invariant Vg5+ gdT cells that are both essential for the development of thymic medullary cells and thus shape the thymic architecture. We further show that all lymphoid progenitors are exclusively of hematopoietic stem cell origin, despite the temporal overlap between thymopoiesis initiation and the transient expression of lymphoid transcripts in yolk sac precursors. This early transient expression does not alter their strict erythro-myeloid differentiation potential. Our work highlights the relevance of the developmental timing on the emergence of different lymphoid subsets required for the establishment of a functionally diverse immune system.