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Burki, Fabien
Publications (10 of 11) Show all publications
Bass, D., Ward, G. M. & Burki, F. (2019). Ascetosporea. Current Biology, 29(1), R7-R8
Open this publication in new window or tab >>Ascetosporea
2019 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. R7-R8Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
CELL PRESS, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-376308 (URN)10.1016/j.cub.2018.11.025 (DOI)000455224500003 ()30620917 (PubMedID)
Available from: 2019-02-05 Created: 2019-02-05 Last updated: 2019-02-05Bibliographically approved
Strassert, J. F. H., Jamy, M., Mylnikov, A. P., Tikhonenkov, D. V. & Burki, F. (2019). New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life. Molecular biology and evolution, 36(4), 757-765
Open this publication in new window or tab >>New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
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2019 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 4, p. 757-765Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2019
Keywords
TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-390283 (URN)10.1093/molbev/msz012 (DOI)000473583700009 ()30668767 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), SNIC 2018/8-192
Available from: 2019-09-09 Created: 2019-09-09 Last updated: 2019-09-09Bibliographically approved
Irwin, N., Tikhonenkov, D., Hehenberger, E., Mylnikov, A., Burki, F. & Keeling, P. (2019). Phylogenomics supports the monophyly of the Cercozoa. Molecular Phylogenetics and Evolution, 130, 416-423
Open this publication in new window or tab >>Phylogenomics supports the monophyly of the Cercozoa
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2019 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 416-423Article in journal (Refereed) Published
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.

Keywords
Cercozoa, Rhizaria, Phylogeny, Phylogenomics, Single-cell transcriptomics
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-374118 (URN)10.1016/j.ympev.2018.09.004 (DOI)000452963200037 ()30318266 (PubMedID)
Available from: 2019-01-23 Created: 2019-01-23 Last updated: 2019-01-23Bibliographically approved
Keeling, P. J. & Burki, F. (2019). Progress towards the Tree of Eukaryotes. Current Biology, 29(16), R808-R817
Open this publication in new window or tab >>Progress towards the Tree of Eukaryotes
2019 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 16, p. R808-R817Article, review/survey (Refereed) Published
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.

Place, publisher, year, edition, pages
CELL PRESS, 2019
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-394146 (URN)10.1016/j.cub.2019.07.031 (DOI)000481587900015 ()31430481 (PubMedID)
Funder
Swedish Research Council, VR-2017-04563Swedish Research Council Formas, 201701197Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2019-10-04 Created: 2019-10-04 Last updated: 2019-10-04Bibliographically approved
Adl, S. M., Bass, D., Lane, C. E., Lukes, J., Schoch, C. L., Smirnov, A., . . . Zhang, Q. (2019). Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology, 66(1), 4-119
Open this publication in new window or tab >>Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
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2019 (English)In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, no 1, p. 4-119Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
Algae, amoebae, biodiversity, ciliate, ecology, flagellate, fungus, microbiology, parasite, plankton, protozoa, systematics, taxonomy
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-376894 (URN)10.1111/jeu.12691 (DOI)000456186200001 ()30257078 (PubMedID)
Funder
EU, Horizon 2020, 679849EU, European Research Council, 771592 CZ 1.05/1.1.00/02.0109 BIOCEVEU, European Research Council, CZ LL1601EU, European Research Council, OPVVV 16_019/0000759Swedish Research Council
Available from: 2019-02-12 Created: 2019-02-12 Last updated: 2019-02-12Bibliographically approved
Whelan, S., Irisarri, I. & Burki, F. (2018). PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics, 34(22), 3929-3930
Open this publication in new window or tab >>PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences
2018 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 22, p. 3929-3930Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
National Category
Bioinformatics and Systems Biology Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-371877 (URN)10.1093/bioinformatics/bty448 (DOI)000450039900023 ()29868763 (PubMedID)
Available from: 2019-01-03 Created: 2019-01-03 Last updated: 2019-01-03Bibliographically approved
Strassert, J. F., Karnkowska, A., Hehenberger, E., del Campo, J., Kolisko, M., Okamot, N., . . . Keeling, P. J. (2018). Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. The ISME Journal, 12, 304-308
Open this publication in new window or tab >>Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates
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2018 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, p. 304-308Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Macmillan Publishers Ltd., 2018
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-334572 (URN)10.1038/ismej.2017.167 (DOI)000418293300026 ()28994824 (PubMedID)
Available from: 2017-11-24 Created: 2017-11-24 Last updated: 2018-01-17Bibliographically approved
Janouskovec, J., Tikhonenkov, D. V., Burki, F., Howe, A. T., Rohwer, F. L., Mylnikov, A. P. & Keeling, P. J. (2017). A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction. Current Biology, 27(23), 3717-3724.e5
Open this publication in new window or tab >>A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction
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2017 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, no 23, p. 3717-3724.e5Article in journal (Refereed) Published
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.

National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-343900 (URN)10.1016/j.cub.2017.10.051 (DOI)000417140100032 ()
Available from: 2018-03-02 Created: 2018-03-02 Last updated: 2018-03-02Bibliographically approved
Janouškovec, J., Gavelis, G. S., Burki, F., Dinh, D., Bachvaroff, T. R., Gornik, S. G., . . . Saldarriaga, J. F. (2017). Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. Proceedings of the National Academy of Sciences of the United States of America, 114(2), E171-E180
Open this publication in new window or tab >>Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
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2017 (English)In: 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) Published
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.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-311779 (URN)10.1073/pnas.1614842114 (DOI)000391439300009 ()28028238 (PubMedID)
Available from: 2017-01-02 Created: 2017-01-02 Last updated: 2017-11-29Bibliographically approved
Burki, F. (2017). The Convoluted Evolution of Eukaryotes With Complex Plastids. In: Yoshihisa Hirakawa (Ed.), Secondary Endosymbioses: (pp. 1-30). Elsevier
Open this publication in new window or tab >>The Convoluted Evolution of Eukaryotes With Complex Plastids
2017 (English)In: 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.

Place, publisher, year, edition, pages
Elsevier, 2017
Series
Advances in Botanical Research, ISSN 0065-2296 ; 84
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-334571 (URN)10.1016/bs.abr.2017.06.001 (DOI)000414512900002 ()978-0-12-802651-9 (ISBN)
Available from: 2017-11-24 Created: 2017-11-24 Last updated: 2018-03-20Bibliographically approved
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