Insights into the phylogenetic and taxonomy of philasterid ciliates (Protozoa, Ciliophora, Scuticociliatia) based on analyses of multiple molecular markers

► Forty eight new sequences for three genes are characterized from 19 taxa of Philasterida. ► BI and ML trees are constructed to assess the relationships of Philasterida. ► AU tests are performed to test the hypothesis of morphology-based classifications. ► Secondary structures of the ITS2 of philasterids are predicted. ► Some conclusions are drawn by comparison among gene trees and morphological systems.