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...