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Most chloroplasts are in the interior cells in leaves, termed the
misspell, and the cells near the surface of green stems. Many leaf and stem epidermal cells lack chloroplasts. The epidermis is the outermost layer of cells on non-woody plant parts. A pair of guard cells surround each leaf stomata. Guard cells usually have chloroplasts. Cells in xylem and phloem tissue also usually lack chloroplasts. Xylem and phloem provide structural support and internal transport of water, minerals and organic compounds in plant organs.

Most underground plant cells lack chloroplasts because chloroplasts require light for their development. Thus, underground organs such as roots, bulbs,tubers, corms and rhizomes would generally lack chloroplasts. However, underground cells often have other kinds of plastids, such as amyloplasts, which store starch. Underground plant organs may develop some chloroplasts if exposed to light.

Window leaf plants have fleshy leaves that are buried in the soil with just the top showing above ground. The window leaves have many cells in the top center of the leaf that are transparent and let light reach the chloroplast-containing cells on the sides of the leaf. The transparent cells lack chloroplasts.

Parasitic plants, such as Indian pipe (Monotropa uniflora) and dodder, lack chlorophyll so have no chloroplasts. White or yellow tissue in variegated-leaf plants also lack chloroplasts. Albino plants also lack chlorophyll. Many non-green flowers and fruits lack chloroplasts at maturity.

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