Serial sectioning of tomograms obtained from flat-embedded flagella of WT and pf28 mutant C. reinhardtii cells showing short IFT trains. The ∼5-nm-thick virtual sections are cut along the longitudinal axis of the axoneme. The three selected cutting planes show ultrastructural features of the short IFT trains that are routinely observed in tomograms obtained from both WT and pf28 flagella. (a–c) Sections of a short train from a WT flagellum. (d–f) Sections of a short train from a pf28 flagellum. Panels a and d show the association of IFT trains with the flagellar membrane. Projections linking the IFT trains to the MT doublet, possibly cytoplasmic dynein 1b because these are retrograde IFT trains, are also visible at this sectioning level. Sections b and e are cut through the axial core of the IFT train, and show the presence of a rodlike structure running parallel to the longitudinal axis of the MT doublet with no internal periodicity. Panels c and f show sections of IFT trains cut through the lollipop-like particles visible along the IFT trains with a 16-nm repeat. (g–i) Colored diagrams superimposed onto panels d–f to highlight the ultrastructural features shown in a–f. White, flagellar membrane; red, IFT train; yellow/brown, MT doublet.