Actually, I would say Linux doesn't have a native GUI, since Qt/GTK are basically cross-platform UI toolkits that sit on top of X11/Wayland/Whatever.
There can't be such thing as native Linux GUI. Linux is a kernel. There is a native Gnome GUI, same for KDE, Unity and probably some other Linux-based desktop environments. X11 is not a "native GUI" either as it is does not have own look & feel.
