Daenerys is a true born Targaryen, but in the last season Jon Snow happened to be the son of Rhaegar Targaryen and Lyanna Stark. So he becomes heir to the throne also. My question is how are these two Targaryen are related?!
Rhaegar was the son of the Mad King Aerys, and older brother to Daenerys and Viserys Targaryen. Lyanna was the only daughter of Rickard Stark, and sister to Ned, Benjen, and Brandon.
Since Jon Snow is the son of Rhaegar and Lyanna, that means Daenerys is his aunt.