We present a novel machine learning approach for data assimilation applied in fluid mechanics, based on adjoint-optimization augmented by Graph Neural Networks (GNNs) models. We consider as baseline the Reynolds-Averaged Navier-Stokes (RANS) equations, where the unknown is the meanflow and a closure model based on the Reynolds-stress tensor is required for correctly computing the solution. An end-to-end process is cast; first, we train a GNN model for the closure term. Second, the GNN model is introduced in the training process of data assimilation, where the RANS equations act as a physics constraint for a consistent prediction. We obtain our results using direct numerical simulations based on a Finite Element Method (FEM) solver; a two-fold interface between the GNN model and the solver allows the GNN's predictions to be incorporated into post-processing steps of the FEM analysis. The proposed scheme provides an excellent reconstruction of the meanflow without any features selection; preliminary results show promising generalization properties over unseen flow configurations.