title: Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista.
abstract: Assembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolutionary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of early diversification events. In this context, the centrohelid heliozoans are particularly relevant for reconstructing the tree of eukaryotes because they represent one of the last substantial groups that was missing large and diverse genomic data. Here, we filled this gap by sequencing high-quality transcriptomes for four centrohelid lineages, each corresponding to a different family. Combining these new data with a broad eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic dataset that enabled us to refine the structure of the tree. Specifically, we show that (i) centrohelids relate to haptophytes, confirming Haptista; (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with Archaeplastida; and (iv) Haptista + SAR is sister to Cryptista + Archaeplastida. The implications of this topology are discussed in the broader context of plastid evolution.
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada burkif@mail.ubc.ca.
authors.forename: Fabien
authors.initials: F
authors.lastname: Burki
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Maia
authors.initials: M
authors.lastname: Kaplan
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.
authors.forename: Denis V
authors.initials: DV
authors.lastname: Tikhonenkov
authors.affiliation: Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
authors.forename: Vasily
authors.initials: V
authors.lastname: Zlatogursky
authors.affiliation: Center for Integrative Bioinformatics, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria.
authors.forename: Bui Quang
authors.initials: BQ
authors.lastname: Minh
authors.affiliation: Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.
authors.forename: Liudmila V
authors.initials: LV
authors.lastname: Radaykina
authors.affiliation: Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Smirnov
authors.affiliation: Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Mylnikov
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, Ontario, Canada pkeeling@mail.ubc.ca.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
mesh_terms: D005075:Biological Evolution; D056890:Eukaryota / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D023281:Genomics; D010802:Phylogeny
keywords: centrohelids; eukaryotes; phylogenomics; plastid evolution; tree of life
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