A cotyledon (pron.: //; "seed leaf" from Greek: κοτυληδών kotylēdōn, gen.: κοτυληδόνος kotylēdonos, from κοτύλη kotýlē "cup, bowl") is a significant part of the embryo within the seed of a plant. Upon germination, the cotyledon may become the embryonic first leaves of a seedling. The number of cotyledons present is one characteristic used by botanists to classify the flowering plants (angiosperms). Species with one cotyledon are called monocotyledonous ("monocots"). Plants with two embryonic leaves are termed dicotyledonous ("dicots") and placed in the class Magnoliopsida.
In the case of dicot seedlings whose cotyledons are photosynthetic, the cotyledons are functionally similar to leaves. However, true leaves and cotyledons are developmentally distinct. Cotyledons are formed during embryogenesis, along with the root and shoot meristems, and are therefore present in the seed prior to germination. True leaves, however, are formed post-embryonically (i.e. after germination) from the shoot apical meristem, which is responsible for generating subsequent aerial portions of the plant.
The cotyledon of grasses and many other monocotyledons is a highly modified leaf composed of a scutellum and a coleoptile. The scutellum is a tissue within the seed that is specialized to absorb stored food from the adjacent endosperm. The coleoptile is a protective cap that covers the plumule (precursor to the stem and leaves of the plant).
Gymnosperm seedlings also have cotyledons, and these are often variable in number (multicotyledonous), with from 2 to 24 cotyledons forming a whorl at the top of the hypocotyl (the embryonic stem) surrounding the plumule. Within each species, there is often still some variation in cotyledon numbers, e.g. Monterey Pine (Pinus radiata) seedlings have 5–9, and Jeffrey Pine (Pinus jeffreyi) 7–13 (Mirov 1967), but other species are more fixed, with e.g. Mediterranean Cypress always having just two cotyledons. The highest number reported is for Big-cone Pinyon (Pinus maximartinezii), with 24 (Farjon & Styles 1997).
The cotyledons may be ephemeral, lasting only days after emergence, or persistent, enduring a year or more on the plant. The cotyledons contain (or in the case of gymnosperms and monocotyledons, have access to) the stored food reserves of the seed. As these reserves are used up, the cotyledons may turn green and begin photosynthesis, or may wither as the first true leaves take over food production for the seedling.
Epigeal versus hypogeal development 
Cotyledons may be either epigeal, expanding on the germination of the seed, throwing off the seed shell, rising above the ground, and perhaps becoming photosynthetic; or hypogeal, not expanding, remaining below ground and not becoming photosynthetic. The latter is typically the case where the cotyledons act as a storage organ, as in many nuts and acorns.
Hypogeal plants have (on average) significantly larger seeds than epigeal ones. They also are capable of surviving if the seedling is clipped off, as meristem buds remain underground (with epigeal plants, the meristem is clipped off if the seedling is grazed). The tradeoff is whether the plant should produce a large number of small seeds, or a smaller number of seeds which are more likely to survive.
Related plants show a mixture of hypogeal and epigeal development, even within the same plant family. Groups which contain both hypogeal and epigeal species include, for example, the Araucariaceae family of Southern Hemisphere conifers, the Fabaceae (pea family), and the genus Lilium (see Lily seed germination types). The frequently garden grown common bean - Phaseolus vulgaris - is epigeal while the closely related runner bean - Phaseolus coccineus - is hypogeal.
The term cotyledon was coined by Marcello Malpighi. John Ray was the first botanist to recognize that some plants have two and others only one, and eventually the first to recognize the immense importance of this fact to systematics.
- Vines, Sydney Howard (1913), "Robert Morison 1620—1683 and John Ray 1627—1705", in Oliver, Francis Wall, Makers of British botany, Cambridge University Press, pp. 8–43
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- Hiroaki Setoguchi, Takeshi Asakawa Osawa, Jean-Christophe Pintaud, Tanguy Jaffré and Jean-Marie Veillon (1998), "Phyloghuhenetic relationships within Araucariaceae based on rbcL gene sequences", American Journal of Botany 85 (11): 1507–1516, doi:10.2307/2446478, JSTOR 2446478, PMID 21680310
- Tiscali.reference - Cotyledon
- Mirov, N. T. (1967). The Genus Pinus. Ronald Press Company, New York.
- Farjon, A. & Styles, B. T. (1997). Pinus (Pinaceae). Flora Neotropica Monograph 75: 221-224.