title: Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages.
abstract: The Ciliophora is one of the most studied protist lineages because of its important ecological role in the microbial loop. While there is an abundance of molecular data for many ciliate groups, it is commonly limited to the 18S ribosomal RNA locus. There is a paucity of data when it comes to availability of protein-coding genes especially for taxa that do not belong to the class Oligohymenophorea. To address this gap, we have sequenced EST libraries for 11 ciliate species. A supermatrix was constructed for phylogenomic analysis based on 158 genes and 42,158 characters and included 16 ciliates, four dinoflagellates and nine apicomplexans. This is the first multigene-based analysis focusing on the phylum Ciliophora. Our analyses reveal two robust superclades within the Intramacronucleata; one composed of the classes Spirotrichea, Armophorea and Litostomatea (SAL) and another with Colpodea and Oligohymenophorea. Furthermore, we provide corroborative evidence for removing the ambiguous taxon Protocruzia from the class Spirotrichea and placing it as incertae sedis in the phylum Ciliophora.
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada. Electronic address: eleni@dal.ca.
authors.forename: E
authors.initials: E
authors.lastname: Gentekaki
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Kolisko
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: V
authors.initials: V
authors.lastname: Boscaro
authors.affiliation: Shannon Point Marine Center, Western Washington University, Anacortes, WA 98221, United States.
authors.forename: K J
authors.initials: KJ
authors.lastname: Bright
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Dini
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Di Giuseppe
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
authors.forename: Y
authors.initials: Y
authors.lastname: Gong
authors.affiliation: School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy.
authors.forename: C
authors.initials: C
authors.lastname: Miceli
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Modeo
authors.affiliation: Protistology Department, American Type Culture Collection, Manassas, VA 20110, United States.
authors.forename: R E
authors.initials: RE
authors.lastname: Molestina
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Petroni
authors.affiliation: School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Pucciarelli
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
authors.forename: A J
authors.initials: AJ
authors.lastname: Roger
authors.affiliation: Shannon Point Marine Center, Western Washington University, Anacortes, WA 98221, United States.
authors.forename: S L
authors.initials: SL
authors.lastname: Strom
authors.affiliation: Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. Electronic address: lynn@zoology.ubc.ca.
authors.forename: D H
authors.initials: DH
authors.lastname: Lynn
mesh_terms: D016798:Ciliophora / Q000145:classification* / Q000235:genetics; D023281:Genomics; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics
chemical_list: D012337:RNA, Ribosomal, 18S
keywords: CONthreeP; Ciliophora; Phylogenomics; Protocruzia; SAL