Comprehensive phylogenomic analyses of ciliated protists with a revised classification of the phylum Ciliophora (Eukaryota, Alveolata).

Phylogenomic analyses are instrumental in enhancing our comprehension of evolutionary relationships across the tree of life. Among eukaryotes, ciliates are one of the most diverse groups of single-cell eukaryotes that play important roles in microbial food webs and have been used as important model organisms in a wide range of studies. However, evolutionary relationships within ciliates remain contentious due to low resolution of limited molecular markers and/or limited taxa. To provide a more comprehensive understanding of the evolutionary relationships within the clade Ciliophora, we sequenced the genomes and/or transcriptomes of 52 ciliate species from 10 classes. Combining analyses of these with publicly available data, we generated a dataset that comprises 190 ciliate species spanning 49 orders, encompassing 16 of the 17 recognized classes within the phylum Ciliophora, thereby achieving nearly complete class-level representation of this diverse group. Among these species, 74 were analyzed for the first time from a phylogenomic perspective. We provided an updated classification of Ciliophora, comprising the class Mesodiniea and two major clades, i.e., Postciliodesmatophora and Intramacronucleata, with Intramacronucleata comprising two main clades (CONthreeP and SLAOMP) and Protocruziea. We also evaluated the effect of missing data and provided datasets-a 200 core-gene family list and multiple sequence alignments-to facilitate future phylogenomic analyses. Furthermore, based on the highly reliable phylogenomic tree, we estimated that the phylum Ciliophora originated approximately 1,052 million years ago (Mya) at the beginning of the Meso-proterozoic period. The robust phylogenomic framework presented here not only facilitates a deeper exploration of ciliate evolution but also provides a reference for future phylogenetic and taxonomic studies.