Hypocotyl
The hypocotyl is the stem of a germinating seedling, found below the cotyledons and above the radicle.
Eudicots
As the plant embryo grows at germination, it sends out a shoot called a radicle that becomes the primary root, and then penetrates down into the soil. After emergence of the radicle, the hypocotyl emerges and lifts the growing tip above the ground, bearing the embryonic leaves, and the plumule that gives rise to the first true leaves. The hypocotyl is the primary organ of extension of the young plant and develops into the stem. The most massive hypocotyl is that of Myrmecodia lamii which can be in height by wide, and is filled with chambers and passageways used by their ant symbiontsMonocots
The early development of a monocot seedling like cereals and other grasses is somewhat different. A structure called the coleoptile, essentially a part of the cotyledon, protects the young stem and plumule as growth pushes them up through the soil. A mesocotyl—that part of the young plant that lies between the seed and the plumule—extends the shoot up to the soil surface, where secondary roots develop from just beneath the plumule. The primary root from the radicle may then fail to develop further. The mesocotyl is considered to be partly hypocotyl and partly cotyledon.Not all monocots develop like the grasses. The onion develops in a manner similar to the first sequence described above, the seed coat and endosperm pulled upwards as the cotyledon extends. Later, the first true leaf grows from the node between the radicle and the sheath-like cotyledon, breaking through the cotyledon to grow past it.