Comment 2 for bug 584964

You may understand it perfectly well, but to some readers it's ambiguous. Adding the comma also helps it to be parsed correctly by machine translators, used by readers who do not have a version of the manual in their native language.

Unless the meaning is:
There are several popular DEs called GNOME; Ubuntu uses one of them
rather than
Ubuntu uses a popular DE; it's called GNOME
adding that comma has more pros than cons.