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  • 1.
    Adl, Sina M.
    et al.
    Univ Saskatchewan, Dept Soil Sci, Coll Agr & Bioresources, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
    Bass, David
    Nat Hist Museum, Dept Life Sci, Cromwell Rd, London SW7 5BD, England;CEFAS, Barrack Rd, Weymouth DT4 8UB, Dorset, England.
    Lane, Christopher E.
    Univ Rhode Isl, Dept Biol Sci, Kingston, RI 02881 USA.
    Lukes, Julius
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic;Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic.
    Schoch, Conrad L.
    Natl Inst Biotechnol Informat, Natl Lib Med, NIH, Bethesda, MD 20892 USA.
    Smirnov, Alexey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Agatha, Sabine
    Univ Salzburg, Dept Biosci, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Berney, Cedric
    CNRS, UMR 7144 AD2M, Grp Evolut Protistes & Ecosyst Pelag, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
    Brown, Matthew W.
    Mississippi State Univ, Dept Biol Sci, Starkville, MS 39762 USA;Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Starkville, MS 39762 USA.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Cepicka, Ivan
    Charles Univ Prague, Dept Zool, Fac Sci, Vinicna 7, CR-12844 Prague, Czech Republic.
    Chistyakova, Lyudmila
    St Petersburg State Univ, Core Facil Ctr Culture Collect Microorganisms, St Petersburg 198504, Russia.
    del Campo, Javier
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Dunthorn, Micah
    Univ Kaiserslautern, Dept Ecol, Erwin Schroedinger St, D-67663 Kaiserslautern, Germany;Univ Duisburg Essen, Dept Eukaryot Microbiol, Univ Str 5, D-45141 Essen, Germany.
    Edvardsen, Bente
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Eglit, Yana
    Dalhousie Univ, Dept Biol, Halifax B3H 4R2, NS, Canada.
    Guillou, Laure
    Univ Paris 06, Sorbonne Univ, Paris 6, CNRS,UMR 7144 AD2M,Stn Biol Roscoff, Pl Georges Teissier,,CS90074, F-29688 Roscoff, France.
    Hampl, Vladimir
    Charles Univ Prague, Dept Parasitol, Fac Sci, BIOCEV, Prumyslov 595, Vestec 25242, Czech Republic.
    Heiss, Aaron A.
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Hoppenrath, Mona
    DZMB German Ctr Marine Biodivers Res, D-26382 Wilhelmshaven, Germany.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Karnkowska, Anna
    Univ Warsaw, Dept Mol Phylogenet & Evolut, PL-02089 Warsaw, Poland.
    Karpov, Sergey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Kim, Eunsoo
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Kolisko, Martin
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic.
    Kudryavtsev, Alexander
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Lahr, Daniel J. G.
    Univ Sao Paulo, Dept Zool, Inst Biosci, Matao Travessa 14 Cidade Univ, BR-05508090 Sao Paulo, SP, Brazil.
    Lara, Enrique
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;CSIC, Real Jardim Bot,Plaza Murillo 2, E-28014 Madrid, Spain.
    Le Gall, Line
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat Evolut Biodiversit, 57 Rue Cuvier,CP 39, F-75005 Paris, France.
    Lynn, Denis H.
    Univ Guelph, Dept Integrat Biol, Summerlee Sci Complex, Guelph, ON N1G 2W1, Canada;Univ British Columbia, Dept Zool, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Mann, David G.
    Royal Bot Garden, Edinburgh EH3 5LR, Midlothian, Scotland;Inst Agrifood Res & Technol, C Poble Nou Km 5-5, E-43540 San Carlos de la Rapita, Spain.
    Massana, Ramon
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Mitchell, Edward A. D.
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;Jardin Bot Neuchatel,Chemin Perthuis du Salut 58, CH-2000 Neuchatel, Switzerland.
    Morrow, Christine
    Natl Museums Northern Ireland, Dept Nat Sci, 153 Bangor Rd, Holywood BT18 0EU, England.
    Park, Jong Soo
    Kyungpook Natl Univ, Sch Earth Syst Sci, Dept Oceanog, Daegu, South Korea;Kyungpook Natl Univ, Sch Earth Syst Sci, Kyungpook Inst Oceanog, Daegu, South Korea.
    Pawlowski, Jan W.
    Univ Geneva, Dept Genet & Evolut, CH-1211 Geneva 4, Switzerland.
    Powell, Martha J.
    Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA.
    Richter, Daniel J.
    Univ Pompeu Fabra, CSIC, Inst Biol Evolut, Passeig Maritim Barceloneta 37-49, Barcelona 08003, Spain.
    Rueckert, Sonja
    Edinburgh Napier Univ, Sch Appl Sci, Edinburgh EH11 4BN, Midlothian, Scotland.
    Shadwick, Lora
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Shimano, Satoshi
    Hosei Univ, Sci Res Ctr, Chiyoda Ku, 2-17-1 Fujimi, Tokyo, Japan.
    Spiegel, Frederick W.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Torruella, Guifre
    Univ Paris XI, Lab Evolut & Systemat, F-91405 Orsay, France.
    Youssef, Noha
    Oklahoma State Univ, Dept Microbiol & Mol Genet, Stillwater, OK 74074 USA.
    Zlatogursky, Vasily V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Zhang, Qianqian
    Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
    Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes2019In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, no 1, p. 4-119Article in journal (Refereed)
    Abstract [en]

    This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

  • 2.
    Bass, David
    et al.
    Ctr Environm Fisheries & Aquaculture Sci Cefas, Barrack Rd, Weymouth, Dorset, England;Nat Hist Museum, Dept Life Sci, Cromwell Rd, London, England.
    Ward, Georgia M.
    Ctr Environm Fisheries & Aquaculture Sci Cefas, Barrack Rd, Weymouth, Dorset, England;Nat Hist Museum, Dept Life Sci, Cromwell Rd, London, England;Univ Exeter, Biosci, Exeter, Devon, England.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ascetosporea2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. R7-R8Article in journal (Other academic)
  • 3.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala Univ, Dept Organismal Biol, Program Systemat Biol, Sci Life Lab, Norbyvagen 18D, S-75236 Uppsala, Sweden..
    Mitochondrial Evolution: Going, Going, Gone2016In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 26, no 10, p. R410-R412Article in journal (Other academic)
    Abstract [en]

    Monocercomonoides is the first example of a eukaryote lacking even the most reduced form of a mitochondrion-related organelle. This has important implications for cellular processes and our understanding of reductive mitochondrial evolution across the eukaryotic tree of life.

  • 4.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The Convoluted Evolution of Eukaryotes With Complex Plastids2017In: Secondary Endosymbioses / [ed] Yoshihisa Hirakawa, Elsevier, 2017, p. 1-30Chapter in book (Other academic)
    Abstract [en]

    The textbook version of how plastids were established by endosymbiosis and subsequently diversified is like a well-oiled machine: a cyanobacterial endosymbiont was taken up by a heterotrophic cell and transformed over time into a bona fide photosynthetic organelle (plastid), ultimately giving rise to all plants and algae. The reality, however, is much more complicated and this chapter attempts to describe recent advances in the field of plastid evolution brought to light by disciplines such as phylogenomics, comparative genomics, and cell biology. If (almost) all plastids may ultimately trace back to the same original endosymbiotic event, the very large diversity of plastids we observe today can only be explained by multiple layers of endosymbioses. That is, plastids were passed between distantly related eukaryotic lineages multiple times, essentially creating a phylogenetic imbroglio where plastids appear monophyletic but hosts are not. The burning question then is: how can we best fit plastid and host data into a comprehensive evolutionary framework? Focusing not only on the so-called complex plastids (the product of eukaryote-to-eukaryote endosymbioses) and the lineages that host them but also on the many related plastid-lacking lineages and orphan taxa, I discuss the emergence of new models of plastid evolution. These models generalize the notion of serial endosymbioses to explain the scattered distribution of plastids in the eukaryotic tree of life. As such, they make new testable predictions as to how complex algae are connected through endosymbiotic gene transfer, but testing this will require first to determine the real magnitude of this process.

  • 5.
    Irwin, Nicholas
    et al.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Tikhonenkov, Denis
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Hehenberger, Elisabeth
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Monterey Bay Aquarium Res Inst, Moss Landing, CA USA.
    Mylnikov, Alexander
    Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Keeling, Patrick
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Phylogenomics supports the monophyly of the Cercozoa2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 416-423Article in journal (Refereed)
    Abstract [en]

    The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas soils, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12' group, and phylogenomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.

  • 6.
    Janouskovec, Jan
    et al.
    UCL, Dept Genet Evolut & Environm, London, England.;San Diego State Univ, Dept Biol, San Diego, CA 92182 USA.;Univ British Columbia, Bot Dept, Vancouver, BC, Canada..
    Tikhonenkov, Denis V.
    Univ British Columbia, Bot Dept, Vancouver, BC, Canada.;Russian Acad Sci, Inst Biol Inland Waters, Borok, Russia..
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ British Columbia, Bot Dept, Vancouver, BC, Canada.
    Howe, Alexis T.
    Univ British Columbia, Bot Dept, Vancouver, BC, Canada..
    Rohwer, Forest L.
    San Diego State Univ, Dept Biol, San Diego, CA 92182 USA..
    Mylnikov, Alexander P.
    Russian Acad Sci, Inst Biol Inland Waters, Borok, Russia..
    Keeling, Patrick J.
    Univ British Columbia, Bot Dept, Vancouver, BC, Canada..
    A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction2017In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, no 23, p. 3717-3724.e5Article in journal (Refereed)
    Abstract [en]

    The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids and re-annotated existing mitochondrial genomes using hidden Markov model gene profiles. This revealed over a dozen previously overlooked mitochondrial genes at the level of eukaryotic supergroups. Analysis of trends over evolutionary time demonstrates that gene transfer to the nucleus was non-linear, that it occurred in waves of exponential decrease, and that much of it took place comparatively early, massively independently, and with lineage-specific rates. This process has led to differential gene retention, suggesting that gene-rich mitochondrial genomes are not a product of their early divergence. Parallel transfer of mitochondrial genes and their functional replacement by new nuclear factors are important in models for the origin of eukaryotes, especially as major gaps in our knowl-edge of eukaryotic diversity at the deepest level remain unfilled.

  • 7. Janouškovec, Jan
    et al.
    Gavelis, Gregory S
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Dinh, Donna
    Bachvaroff, Tsvetan R
    Gornik, Sebastian G
    Bright, Kelley J
    Imanian, Behzad
    Strom, Suzanne L
    Delwiche, Charles F
    Waller, Ross F
    Fensome, Robert A
    Leander, Brian S
    Rohwer, Forest L
    Saldarriaga, Juan F
    Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 2, p. E171-E180Article in journal (Refereed)
    Abstract [en]

    Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.

  • 8.
    Keeling, Patrick J.
    et al.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Progress towards the Tree of Eukaryotes2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 16, p. R808-R817Article, review/survey (Refereed)
    Abstract [en]

    Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.

  • 9.
    Strassert, Jürgen F. H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jamy, Mahwash
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mylnikov, Alexander P.
    Russian Acad Sci, Inst Biol Inland Waters, Borok, Yaroslavl Regio, Russia.
    Tikhonenkov, Denis V.
    Russian Acad Sci, Inst Biol Inland Waters, Borok, Yaroslavl Regio, Russia.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 4, p. 757-765Article in journal (Refereed)
    Abstract [en]

    The resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these "orphan" groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker "TSAR" to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

  • 10.
    Strassert, Jürgen F H
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Karnkowska, Anna
    Hehenberger, Elisabeth
    del Campo, Javier
    Kolisko, Martin
    Okamot, Noriko
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Janouškovec, Jan
    Poirier, Camille
    Leonard, Guy
    Hallam, Steven J
    Richards, Thomas A
    Worden, Alexandra Z
    Santoro, Alyson E
    Keeling, Patrick J
    Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, p. 304-308Article in journal (Refereed)
    Abstract [en]

    Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.

  • 11.
    Whelan, Simon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Irisarri, Iker
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences2018In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 22, p. 3929-3930Article in journal (Refereed)
    Abstract [en]

    A Summary: Phylogenomic datasets invariably contain undetected stretches of non-homologous characters due to poor-quality sequences or erroneous gene models. The large-scale multi-gene nature of these datasets renders impractical or impossible detailed manual curation of sequences, but few tools exist that can automate this task. To address this issue, we developed a new method that takes as input a set of unaligned homologous sequences and uses an explicit probabilistic approach to identify and mask regions with non-homologous adjacent characters. These regions are defined as sharing no statistical support for homology with any other sequence in the set, which can result from e.g. sequencing errors or gene prediction errors creating frameshifts. Our methodology is implemented in the program PREQUAL, which is a fast and accurate tool for high-throughput filtering of sequences. The program is primarily aimed at amino acid sequences, although it can handle protein coding DNA sequences as well. It is fully customizable to allow fine-tuning of the filtering sensitivity.

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