The three sisters refer to corn, beans and squash. They were considered sisters because when grown together they are inseparable, giving and providing for each other, just like human sisters. When planted together, each brings their own strengths and weaknesses, mutually providing for and taking from each other, allowing all to thrive.
The Bean plant climbed on the cornstalk. The Squash plant provides shade for the roots of the beans and corn. And they all provide nutrients into the soil for each other.