Comparative genomics reveals insights into the ultrafast Ca2+-dependent cell contraction in ciliates (Eukaryota, SAR, Alveolata)

Certain ciliate taxa possess a Ca²⁺-dependent mechanism for ultrafast contraction, in addition to the more common adenosine triphosphate (ATP)-dependent process. In this study, we integrated omics data from 47 ciliate species, focusing on four target ciliate taxa: Vorticellidae, Zoothamniidae, Stentor, and Spirostomum. The spasmin gene, which encodes a key calcium-binding protein, was detected in 17 oligohymenophoreans (13 peritrichs, two peniculians, and two scuticociliatians) and three heterotricheans (one Stentor and two Spirostomum species). Gene family analysis revealed a roughly proportional relationship between genome/transcriptome size and the number of expanded gene families in these four target taxa. Functional enrichment analyses of significantly expanded gene families indicated rapid evolution of genes associated with phosphatase activity, dephosphorylation, signal transduction, metabolism, and transport. These findings provide new insights into the genomic adaptations underlying the unique contractile mechanisms of these ciliates.