Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

E Gentekaki; M Kolisko; V Boscaro; K J Bright; F Dini; G Di Giuseppe; Y Gong; C Miceli; L Modeo; R E Molestina; G Petroni; S Pucciarelli; A J Roger; S L Strom; D H Lynn

doi:10.1016/j.ympev.2014.04.020

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

Mol Phylogenet Evol. 2014 Sep:78:36-42. doi: 10.1016/j.ympev.2014.04.020. Epub 2014 May 6.

Authors

E Gentekaki¹, M Kolisko², V Boscaro³, K J Bright⁴, F Dini³, G Di Giuseppe³, Y Gong⁵, C Miceli⁶, L Modeo³, R E Molestina⁷, G Petroni³, S Pucciarelli⁶, A J Roger⁸, S L Strom⁴, D H Lynn⁹

Affiliations

¹ Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada. Electronic address: eleni@dal.ca.
² 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.
³ Department of Biology, University of Pisa, Pisa 56126, Italy.
⁴ Shannon Point Marine Center, Western Washington University, Anacortes, WA 98221, United States.
⁵ The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
⁶ School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy.
⁷ Protistology Department, American Type Culture Collection, Manassas, VA 20110, United States.
⁸ Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
⁹ Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada. Electronic address: lynn@zoology.ubc.ca.

PMID: 24814356
DOI: 10.1016/j.ympev.2014.04.020

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.

Keywords: CONthreeP; Ciliophora; Phylogenomics; Protocruzia; SAL.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ciliophora / classification*
Ciliophora / genetics
Genomics
Phylogeny*
RNA, Ribosomal, 18S / genetics

Substances

RNA, Ribosomal, 18S