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Heterokont cells have two unequal flagella, inserted subapically or laterally, which in most are anchored by four microtubule roots in a characteristic pattern. One flagellum extends forward, and is covered by lateral mastigonemes or bristles, which have a unique tripartite structure. When the flagellum moves these create a backwards current, pulling motile cells forwards, while in their absence the opposite would be the case. The other flagellum is smooth and usually shorter, sometimes reduced to a basal body. There are a number of variations on this basic pattern. The mastigonemes are composed of glycoproteins and are made in the endoplasmic reticulum, then transported to the cell surface. Many stramenopiles also have scales, spines, or shells, which may be organic or siliceous.
When present, chloroplasts are bound by four membranes, of which the outermost is continuous with the endoplasmic reticulum. They contain chlorophylls a and c, and usually the carotenoid fucoxanthin, which gives them a golden-brown colour. These appear to be derived from some red alga, though its nucleus has not been retained. Similar chloroplasts are found among the haptophytes and cryptomonads, and these are sometimes supposed to share a common coloured ancestor with the stramenopiles, in which case they may be grouped as the chromists. However, there are some notable differences between these groups, and the coloured stramenopiles appear to form a monophyletic subgroup, suggesting they acquired chloroplasts independently.
Most heterokont algae were originally grouped in the division Chrysophyta and the class Chrysophyceae, called golden algae, with the diatoms treated as a separate class and the brown algae as a separate division. The golden algae are paraphyletic, however, and have since splintered into a number of groups, variously treated as separate classes of Chrysophyta, separate divisions, or as classes of a single division Heterokontophyta or Chromophyta. The various lines of such algae include the following:
The other groups lack chloroplasts, and some do not have the typical heterokont organization in flagellate cells, but their relationship with the other stramenopiles is supported by structural and molecular studies. These groups include the following: