The cell wall is composed of complex polysaccharides, and is assembled by fusion of discrete particles. This type of wall is considered homologous to the scaly coverings of "prasinophyte" green algae, not to the microfibrillar cell walls of higher plants and many multicellular green algae.

The flagellate cell cytoskeleton is based on a symmetrical array of two flagellar bases, four microtubular roots and one centrin-based striated root.

The flagellar bases form a "V"; algae in which the bases form other patterns, or are separate from each other, belong to different genera. The bases are not colinear, but diverge from each other in the clockwise direction by about 120 nm (half the diameter of the flagellar base); algae that do not have this "clockwise absolute configuration" belong to other genera. The proximal ("bottom") ends of the flagellar bases are connected to each other by two striated proximal connecting fibers, and to the nucleus by the striated rhizoplast. The distal ("top") ends of the basal bodies are connected by a single striated distal connecting fiber. Both the rhizoplast and the distal connecting fiber are known to contain the contractile protein centrin.

Two microtubular roots are associated with each basal body. One root has two microtubules and is associated with a striated fiber, while the other has four microtubules that lie in a three-over-one arrangement near the basal bodies.

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