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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.
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