A revised taxonomy and phylogeny of opalinids (Stramenopiles, Opalinata) inferred from the analysis of complete nuclear ribosomal DNA (rDNA) genes - alignments and phylogenetic trees

The data include 1) the sequence alignments of the SSU rDNA gene and of the ITS-LSU rDNA gene of opalinids, proteromonads and related species, in fasta format and formatted for MEGA-X ('?' added). 2) the phylogenetic trees obtained in MEGA-X by using the sequence alignments (SSU and ITS-LSU) and the maximum likelihood and maximum parsimony methods, and the trees obtained in MrBayes by using the bayesian inference method. 3) The trees obtained in the timetree analysis made in MEGA-X with the SSU rDNA alignment. Three groups of time calibration points were used: A, "sequence evolution" group, included calibrations for the Apicomplexa-Dinoflagellata divergence, Ciliophora divergence, and Stramenopiles divergence nodes; B, "host Class constraints" include calibrations for the Karotomorpha and Proteromonas divergence nodes, based on the maximum estimated time of emergence of amphibians (for the Karotomorpha node) and sauria (for the Proteromonas node); and C, "host family constraints" include calibrations for the Protoopalina and Opalina-Zelleriella nodes based on the estimated time of emergence of the most ancient anuran family in which each genus has been cited. Four scenarios were considered (the timetree obtained in each scenario is provided): scenario 1, only calibration points of group A; scenario 2, groups A-B; scenario 3, groups A-C; scenario 4, groups A-B-C.