Ciliates are an ancient and highly diverse group of unicellular eukaryotes that hold significant value in various fields of research such as ecology, evolutionary biology, and epigenetics. With the advancement of sequencing technology and deeper research into ciliates, an increasing amount of omics data have been generated. Here we compiled high-throughput sequencing data from 96 functional gene knockdown or knockout experiments in three genetically manipulable model ciliates, Tetrahymena thermophila, Paramecium tetraurelia, and Oxytricha trifallax, as well as other omics data from 69 ciliate species, to establish a functional genomics database for ciliates (CiliateBase; available at http://ciliatebase.maolab.org/). CiliateBase integrates various data types, including RNA-seq, ChIP-seq, MNase-seq, and RIP-seq, to analyze the functional genes and regulatory networks in ciliates. It provides tools for gene expression analysis, Gene Ontology (GO) enrichment analysis, and KEGG pathway enrichment analysis. With its user-friendly interface and powerful data visualization tools, CiliateBase enables researchers to easily search and analyze functional genomics data. It also supports downloading raw data and processed results, significantly facilitating the progress of ciliate research. In summary, CiliateBase provides a robust resource for functional genomics studies of ciliates.

Psammophillic ciliates are an integral part of the foodweb despite being underrepresented in terms of molecular phylogeny and modern taxonomy. To investigate the karyorelictean group, sampling was conducted in interstitial marine habitats in China for ciliates living between the sand grains, resulting in an examination of the families Cryptopharyngidae Jankowski, 1980 and Kentrophoridae Jankowski, 1980. Three species, i.e., Cryptopharynx setigerus Kahl, 1928, Kentrophoros fasciolatus (Sauerbrey, 1928) Foissner, 1995 and K. fistulosus (Fauré-Fremiet, 1950) Foissner, 1995, are clearly recognized as being cosmopolitan, while other species await further recording. Phylogenetic analyses were carried out based on updated data. These revealed that the families Cryptopharyngidae and Kentrophoridae are closely related, and most genera studied are monophyletic, although Cryptopharynx qingdaoensis n. sp. is located within the Kentrophoridae branch. Brief revisions of two genera, namely Cryptopharynx Kahl, 1928 and Kentrophoros Sauerbrey, 1928, are provided including keys to the identification of nine species belonging to the former and 12 species belonging to the latter. One new genus, Parakentrophoros n. gen., and one new species, Cryptopharynx qingdaoensis n. sp., are described and a new combination, Parakentrophoros canalis (Wright, 1982) n. comb., is established. Finally, it appears that the subapical oral apparatus undergoes a gradual degeneration process from Cryptopharyngidae to Kentrophoridae.