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The stem is the aerial part of the plant that support other aerial organs like leaves, flowers, fruits and seeds. Some species have underground stems. Other functions of the stem are conducting substances, photosynthesis and storing. The final morphology of the stem (height, width, robustness, branching pattern) depends on the interaction between the genetic information and environmental conditions.

In the embryo, the stem is known as plumule. Epicotyl is the embryo shoot above cotyledons, and it has the caulinar meristem at the tip, which is protected by undifferentiated leaves known as primordial leaves. After germination, the caulinar apical meristem is responsible for the increase in length of the stem, forming the nodes and internodes (Figure 1). Nodes are the places where the leaves and lateral branches are inserted. The axillary buds are composed of a group of cells that form a meristm and several primordial leaves protecting the meristem. Axillary buds are found at the insertion point of leaves and lateral branches in the nodes and give rise to lateral branches and flowers. Internodes are the stem regions between nodes. They lack lateral organs. It can be said that the stem is made up of nodes, internodes and axillary buds tidily arranged. Phytomer consists of a node, an internode region and axillary buds that is repeated along the stem. This modular design facilitates the construction of shoots and plant adaptation to the environment.

Figure 1. Stem structure.

Two types of growing happen in stems: primary and secondary. Primary growth is found in the initial growing of every stem, when the stem tissues are directly differentiated from the shoot apical meristem. This meristem is more complex that the root apical meristem because it gives rise to all stem tissues, leaf primordia and axillary buds of the nodes. It means that it is responsible for all the lateral organs of the stem. The shoot apical meristem does not show any protective covering. Intercalary meristem is derived from the shoot apical meristem. It is first found in the internode region and later at the base, close to the node. Most of the growing in length of the stem is derived of the activity of the intercalary meristem. Most dicot and gymnosperm plants show a secondary growth, which increases the diameter of the stem. This growing is produced by the activity of secondary meristems: vascular cambium and cork cambium. In monocot plants, the secondary growth is supposed that was lost during evolution because all the procambium is differentiated in vascular tissue, instead of remaining as undifferentiated tissue. However, some monocot plants have developed a lateral meristem, known as peripheral growing meristem, which produces vascular bundles with the phloem wrapped by the xylem.

The branches of the stem emerge from the axillary buds. However, those axillary buds close to the shoot apical meristem do not form branches because it releases inhibitory substances. This inhibition is known as apical dominance. As the shoot grows in length the shoot apical meristem separates from the already formed axillary buds, and the apical dominance gets attenuated. Thus, axillary buds develop into branches. There are plants without lateral branches, like palms.

In some plant species, there are specialized structures in the stem, such as tendrils of ivy and vine , which are intended for support. There are also thorns in rose stems for protection (thorns are not modified leaves), and cladodes of Asparagales that work as leaves, but they are not.

Besides conduction and support, stems may be specialized in other functions. In some species the stem is a sophisticated storing organ. For example, potatoes have underground stems specialized in storing starch, which are what we eat. Most of a potato is actually storage parenchyma under the epidermis. The potato "eyes" are the axillary buds. Other species have the stem partially buried and the aerial parts are lost during winter. Thus, the underground stem survives the winter and sprouts new aerial organs in wpring. These stems are known as corms. Some xerophytes have stems specialized in storing water. The stems of prickly pears (cactus) look like large and thick leaves, but actually the leaves are the spines.

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