Board Thread:Naruto Discussions/@comment-5413572-20140703171400/@comment-3279282-20140704134757

Imagine: There was a tree without eye, but with Chakra fruit. Kaguya ate the fruit, which resulted in the Rinnegan and thus the TT's Rinnegan. When the TT was made into the tree again, it kept the Rinnegan. This is simply based on the fact that the tree nowadays doesn't look like the original tree at all. There is a high possibility that it didn't have the eye before Kaguya ate its fruit.