Foraminifera and radiolarians are closely related amoeboid protists (i.e., retarians) often characterized by their shells and pseudopodia. Previous studies hypothesized that the unusual "Type 2" β-tubulin (β2) is critically involved in forming helical filaments (HFs), a unique microtubule (MT) assembly/disassembly intermediate found in foraminiferan reticulopodia. Such noncanonical β-tubulin sequences have also been found in two radiolarian species and appear to be closely related to the foraminiferan β2. In this study, we report 119 new β-tubulin transcript sequences from six foraminiferans, four radiolarians, and a related non-retarian species. We found that foraminiferan and radiolarian β2-tubulins share some of the unusual substitutions in the structurally essential and usually conserved domains. In the β-tubulin phylogeny, retarian β2-tubulin forms a monophyletic clade, well separated from the canonical β-tubulin (β1) ubiquitous in eukaryotes. Furthermore, we found that foraminiferan and radiolarian β2-tubulin lineages were under positive selection, and used homology models for foraminiferan α- and β-tubulin hexamers to understand the structural effect of the positively selected substitutions. We suggest that the positively selected substitutions play key roles in the transition of MT to HF by altering the lateral and longitudinal interactions between α- and β-tubulin heterodimers. Our results indicate that the unusual β2-tubulin is a molecular synapomorphy of retarians, and the β-tubulin gene duplication occurred before the divergence of Foraminifera and radiolarians. The duplicates have likely been subjected to neofunctionalization responsible for the unique MT to HF assembly/disassembly dynamics, and/or other unknown physiological processes in retarian protists.
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