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Background  Cilia emanate from basal bodies just underneath the cell membrane. Basal bodies must withstand torque from the ciliary beat and be appropriately spaced for cilia to beat in metachronal waves. Basal body rootlets provide stability for motile cilia.  Paramecium  has three. Our focus is on the largest one, the striated rootlet (SR).  Paramecium  basal bodies align in straight rows. Previously we found a potential role for the SR in this alignment. Here we present a phylogeny of the  Paramecium  homologs of the  SF - Assemblin  gene of the SR of  Chlamydomonas,  and the organization of these genes. We describe the phenotypes from RNA interference (RNAi) silencing of genes and gene groups.    Methods  Phenotypes of the RNAi depletions were characterized by immunofluorescence (IF), electron microscopy, and mass spectrometry.    Results  We found 30 genes for  Paramecium  SF-Assemblin homologs ( SFA ) organized into 13 Paralog Groups (further categorized in five Structural Groups). Representatives of Paralog Groups were found in the SRs. Silencing the transcripts of any of the Structural Groups correlates with misaligned rows of basal bodies, SRs, and cortical units. The silencing of Structural Groups was key and gave us the ability to systematically disrupt SR structures and cell surface organization.    Conclusions  Silencing of  SFA  genes and Paralog Groups shows no effects on the SR or the cell surface organization. Silencing of the larger Structural Groups has an enormous impact on rows of basal bodies, SRs and cortical units, and SR striations, and length. Misaligned basal bodies have cilia causing the cells to swim in abnormal paths.

SF-Assemblin genes in Paramecium: phylogeny and phenotypes of RNAi silencing on the ciliary-striated rootlets and surface organization