Many leaves produce water-soluble vacuolar pigments, which are stored within cell vacuoles (microscopic water sacs within each cell), not the plastids. Two major classes of leaf vacuolar pigments are anthocyanins (and a few other flavonoids) and betalains. Either may be present as pigments along the petiole and major veins, as well as the young stem (Examples: cultivated radish and Rumex hymenosepalus), coloring the entire leaf blade (Examples: Setcreasea pallida, a bromeliad, the snow plant (Sarcodes sanguinea), and an acanth), and the lower leaf (Miconia calvescens and a tropical euphorb).
Anthocyanins are pink, red, purple, and blue pigments (flavonoid chemistry) that occur in many species of land plants. Normally, anthocyanins are most commonly observed as coloration of flowers and fruits, imparting the red color of many berries, for example. Flavonoids other than the anthocyanins generally are colorless, and therefore are not pigments, but there are a few that are yellow compounds and certain flavones are responsible for whites. Flavonoids are pigments that are not involved at all in photosynthesis (unlike plastid pigments), but especially the colorless flavonoids, often abundant in leaf cuticle and epidermis, appear to function as screens for ultraviolet radiation.
Betalains are an unrelated class of nitrogen-containing vacuolar pigments (betalain chemistry and biosynthesis), and they occur in only one major lineage of dicotyledons, the centrosperms, which includes cacti (Examples: beaver-tail cactus, hedgehog cactus, and an Arizona cactus), bougainvillea, portulaca, ice plants, and beets. Betalains may be purple to red (base forms, betacyanins), orange to yellow (acid forms, betaxanthins), and often the color is bright and vibrant.
Especially anthocyanins have been seen in the United States as pigments of young leaves emerging in springtime (Examples: Dombeya ianthotricha, Rhapiolepis indica, evergreen grape, ash, bougainvillea, photinia, creeping fig, and a fern) and again in the fall, as leaves senescence (Examples: Asian cherry and poison sumac). Scientists have determined that this is a response to short daylength in some plants. Why vacuolar pigments are expressed during springtime, when sunlight intensity is relatively low, remains an unanswered question. In the fall, especially anthocyanins are the responsible pigment for reds in leaves of deciduous woody plants. These vacuolar pigments are seen when the chlorophyll degrades during leaf senescence, at which time nitrogen in the leaf is transported out of the leaf for use or storage elsewhere. Although some leaves have anthocyanins in leaf tissues throughout the life of the leaf, as in Miconia calvescens and Abelia, there are many plants in which the vacuolar pigments are synthesized in old leaves (a tropical euphorb).
Anthocyanins and betalains are commonly seen in shoots of plants that have been exposed to environmental stress, such as cold shock, exposure to salt, low light intensity, and water stress. Whether this is a special ecological or physiological strategy is still unknown.
Many tropical plants produce a flush of leaves, a rapid spurt of new growth having leaves that are markedly red or purple when young, not green (Examples: mango, Talauma hodgsonii, and Miconia calvescens). The red coloration is produced most commonly by vacuolar pigments. Although anthocyanins could be an ultraviolet screen, the most popular hypothesis is that these are "cheap leaves" for a plant. A developing leaf, which would be a tender meal for herbivores, forms its cells cheaply before the nitrogen-rich chlorophyll is made. Nongreen flushes are common in lowland tropical forest plants. Nonetheless, this hypothesis is still being tested and the answer may not be as simple as once thought.
Numerous species in tropical forest understory have leaves that are green on the upper side and bright purple on the lower side (Example: a rain forest plant) or are distinctly red-purple on top and bottom of the leaf (Calathea). Because the forest floor has very low light (low photon flux density, PFD), some authors have hypothesized that the additional pigmentation may be a way to reflect light waves back into the photosynthetic cells of the leaf, but the evidence favoring this interpretation is not particularly solid.
Certain monocotyledons have leaves that are maculate, i.e., spotted with red spots and patches (Example: Manfreda maculata). Other places with vacuolar pigments are utilized for patchy color is on the "pitchers" of certain insectivorous plants (Examples: Sarracenia purpurea and Nepenthes). In a group of succulent plants from desert regions, living stones live mostly buried in the ground and use special coloration to disguise leaves, i.e., cryptic coloration to appear like soil and stones.