Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

Recent high-throughput sequencing endeavors have yielded
multi-gene/protein phylogenies that confidently resolve several inter- and
intra-class relationships within the phylum Ciliophora.  We
leverage the massive sequencing efforts from the Marine Microbial
Eukaryote Transcriptome Sequencing Project, other SRA submissions, and
available genome data with our own sequencing efforts to determine the
phylogenetic position of Mesodinium and to generate the most
taxonomically-rich phylogenomic ciliate tree to date.  Regardless
of the data mining strategy, the multi-protein dataset, or the molecular
models of evolution employed, we consistently recovered the same
well-supported relationships among ciliate classes, confirming many of the
higher-level relationships previously identified.  Mesodinium
always formed a monophyletic group with members of the Litostomatea, with
mixotrophic species of Mesodinium – M. rubrum, M. major, and M. chamaeleon
- being more closely related to each other than to the heterotrophic
member, M. pulex.  The well-supported position of Mesodinium as
sister to other litostomes contrasts with previous molecular analyses
including those from phylogenomic studies that exploited the same
transcriptomic databases.  These topological discrepancies
illustrate the need for caution when mining mixed-species transcriptomes
and indicate that identifying ciliate sequences among prey contamination -
particularly for Mesodinium species where expression from stolen prey
nuclei appears to dominate – requires thorough and iterative vetting with
phylogenies that incorporate sequences from a large outgroup of prey.