Shoots are classified based on whether the cotyledons (seed leaves) are carried above ground or remain below ground. Seed germination during which the cotyledons are carried above ground is called epigeous. The food stored in the cotyledons is digested, and the products are transported to the growing parts of the young seedling. When the seedling becomes established and is no longer dependent upon the stored food in the seed for nutrition, the cotyledons gradually decrease in size, wither, and fall off.

Seed germination during which the cotyledons remain underground is called hypogeous. The seedling uses the stored food from the cotyledons for growth, then the cotyledons decompose. The cotyledons remain in the soil during the entire process.