$E_6$ Yukawa couplings in F-theory as D-brane instanton effects

In a weak coupling limit the neighborhood of $E_6$ Yukawa points in $SU(5)$ GUT F-theory models is described by a non-resolvable orientifold of the conifold. We explicitly show, first directly in IIB and then via a mirror symmetry argument, that in this limit the $E_6$ Yukawa coupling is better described as coming from the non-perturbative contribution of a euclidean D1-brane wrapping the non-resolvable cycle. We also discuss how the M-theory description interpolates between the weak and strong coupling viewpoints.