Place beets in a large pot and cover with about 2 inches of water. Bring to boil. Reduce heat and simmer for about 30 minutes until beets are soft and can be easily pierced with a knife. Remove from heat, drain, and allow beets to cool for 15-20 minutes. Once cool enough to touch, remove skins and place in a food processor. Blend until smooth. Set aside.
Preheat the oven to 350 degrees Fahrenheit. Spray a 10" bundt pan and set aside.
In a large bowl combine flour, cocoa powder, sugar, baking soda, baking powder, and salt. In a separate whisk together beet puree, apple sauce, water, canola oil, and vanilla extract. Add the wets to the dries and mix until just combined. Fold in the chocolate chips.
Pour the batter into the prepared Bundt pan and bake for about 45-60 minutes, until a toothpick inserted in the middle comes out clean. Remove from oven and allow to cool in the pan for 20 minutes. Flip out onto a cooling rack and cool completely.
Follow these instruction to make the Chocolate Ganache. Pour over cooled cake and serve.