transcriptome; FHL2. 25 26 Abbreviations: DEG, differentially-expressed gene; FHL2, Four-and-a-half LIM domain 2; 27 iNKT, invariant Natural Killer T cell; IL-, interleukin-; IFN, interferon; PAGA, partition-based 28 graph abstraction; TCR, T cell receptor; TF, transcription factor; WT, wild-type 29 30 31 32 33 34 2 Summary 35 CD1d-restricted invariant Natural Killer T (iNKT) cells represent a unique class of T 36 lymphocytes endowed with potent regulatory and effector immune functions. Although these 37 functions are acquired during thymic ontogeny, the sequence of events that give rise to discrete 38 effector subsets remains unclear. Using an unbiased single-cell transcriptomic analysis 39 combined with functional assays, we revealed an unappreciated diversity among thymic iNKT 40 cells, especially among iNKT1 cells. Mathematical modelling and biological methods 41 unravelled a developmental map whereby iNKT2 cells constitute a transient branching point 42 towards the generation of iNKT1 and iNKT17 cells, which reconciles the two previously 43 proposed models. In addition, we identified the transcription co-factor Four-and-a-half LIM 44 domains protein 2 (FHL2) as a critical cell-intrinsic regulator of iNKT1 specification. Thus, 45 these data illustrate the changing transcriptional network that guides iNKT cell effector fate. Type I or invariant (i) Natural Killer T (iNKT) cells are a versatile population of thymus-derived 70 αβT cells that play a critical role in the initiation and orchestration of immune responses in 71 many pathological contexts including infection, cancer, inflammation and metabolic disorders 72 (Bendelac et al., 2007; Godfrey et al., 2010). iNKT cells respond to lipid-based antigens 73 presented by the quasi-monomorphic MHC class I-related CD1d molecule (Bendelac et al., 74 2007). Their swift response in the periphery is largely dependent on the existence of discrete 75 pre-set subsets that secrete substantial amounts of either interleukin 4 (IL-4), IL-17A/F or 76 interferon-γ (IFN-γ) akin to MHC-restricted T-helper cells and innate lymphoid cells (ILCs). 77 This functional segregation is believed to be instigated in the thymus during their development 78 involving many cues such as self-antigen recognition, transcription factors (TF), cytokine 79 receptor signalling and cell-cell interactions. 80 The developmental steps underlying iNKT cell differentiation remain controversial. Two non-81 mutually exclusive models have been proposed. Initially, a linear maturation model has been 82 reported (Benlagha et al., 2002; Pellicci et al., 2002) in which newly-selected stage 0 (CD24 + ) 83 iNKT cells mature through stages 1 to 3 with the loss of CD24 expression and the sequential 84 acquisition of CD44 and NK1.1. Functionally, iNKT cell maturation through these stages is 85 associated with a reduced capacity to produce IL-4 and concomitant increase in IFN-γ 86 production, which implies that IL-4-producing iNKT cells (comprised in stage 2) constitute an 87 immature pool of cells. A more recent line...