A rotten plant is a new plant that will generate in your caves. It can only survive when it isn't very light. The left picture under here is when it isn't done and the right when it is.
Rotten done

When you destroy any of these plants it will drop rotten seed and when you destroy the right one it will also drop rotten flesh.

Rotten flesh can be cooked into cooked flesh like this.

Cooked flesh