The cytoskeleton of flagellate chromophyte algae, zoospores and gametes is active during swimming, phototaxis, several types of phagotrophic feeding, the formation, secretion and deployment of silica-scales, and the abrupt movement of spine-scales. The flagellar basal bodies are anchored by microtubular roots and/or fibrous roots. The kinds, numbers, and paths of these roots are characteristic of different taxonomic groups within the chromophytes. There are more differences in flagellar apparatuses for taxonomic classes dominated by flagellates as compared to classes dominated by coccoid, filamentous, or parenchymatous forms. Swimming cells that exhibit phototaxis often contain an autofluorescent substance that is located at the base of one flagellum. Phagotrophy occurs in flagellates of several distantly related taxonomic classes, suggesting that phagotrophy evolved independently several times. The most complex phagotrophic process occurs in the Chrysophyceae where one microtubule of a flagellar root forms a feeding basket or pouch into which food particles are moved. The silica-scales of the Synurophyceae are formed, secreted and finally moved into position outside the cell by cytoskeletal components. The six spine-scales of Apedinella (Pedinellophyceae) lie outside the plasma membrane, but they are attached by microligaments and are repositioned almost instantly by a cytoskeletal complex of actin, centrin, and microtubules. A phylogenetic classification based upon a cladistic analysis suggests that aquatic fungi are natural members of the chromophyte group.
