| 1. |
- Adl, Sina M., et al.
(författare)
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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
- 2019
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Ingår i: Journal of Eukaryotic Microbiology. - : WILEY. - 1066-5234 .- 1550-7408. ; 66:1, s. 4-119
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Al Jewari, Caesar
(författare)
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Resolving deep nodes of eukaryote phylogeny
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- My thesis aims to solve deep nodes in the eukaryote tree of life (eToL), by developing new data sets and new approaches to analysing them. In paper I, I described a dataset of 76 universal eukaryotic proteins of bacterial descent (euBacs), in order to test the relations among the three main divisions of mitochondriate eukaryotes (Amorphea, Diaphretickes and Discoba). I developed two protocols to identify problematic data. The conJac protocol analyzes data by jackknifing to detect outlier sequences, while conWin uses a sliding window to find sequence fragments of potentially foreign origin. Phylogenetic analyses of the 76 euBacs, with and without conWin or conJac filtering place Discoba as the sister group to Amorphea and Diaphretickes. The results are largely consistent and highly supported under various evolutionary models except for highly complex CAT models. In paper II, I describe a dataset of 198 universal eukaryote proteins of archaeal ancestry (euArcs), which includes the remaining eukaryotes, informally referred to as amitochondriate excavate. These were excluded from the previous study because they lack euBacs. Phylogenetic analyses of the euArc dataset place the amitochondriate excavate as the first three branches of eToL, followed by Discoba, the only mitochondriate excavates, which appear as a sister group to the remaining eukaryotes. I also developed a protocol using predicted protein structures to increase the fitness of the model without inflating the parameter space, allowing me to conduct a series of control analyses and further support the multi-excavate root. In Paper III, I describe a new application of reciprocal-rooting using concatenated sequences, which I then use to test the euArc root. I also developed two sampling protocols unique to this kind of data. The protocols confirm the multi-excavate euArc root, which indicates that eukaryotes arose from an excavate ancestor. Paper IV describes a follow-up on the ConWin results from Paper I. These show moderate to strong support for mosaicism in 16 euBac proteins from diverse metabolic pathways and donor lineages. In summary, this thesis presents a novel root for the eukaryote tree of life. The new root requires revision of fundamental theories of eukaryote evolution including the source and timing of mitochondrial origins. The methods I have developed are applicable to many different kinds of phylogenetic studies, and the new protein structure model should make these analyses faster, more flexible, and more widely available.
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| 3. |
- Alfjorden, Anders, et al.
(författare)
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Identification of a new gregarine parasite [Apicomplexa, Alveolata] in mass mortality events of freshwater pearl mussels (Margaritifera margaritifera)
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The freshwater pearl mussel (FPM) Margaritifera margaritifera is a Holarctic species with key roles in river ecosystems. Although of highly ecological importance the species is globally threatened and reaching nearing extinction in Europe. FPM is particularly vulnerable to fluctuations of environmental conditions, being entirely dependent of highly oxygenated streams with clear running water. Therefore anthropogenic activities resulting in habitat loss or affecting water quality such as sedimentation, eutrophication, or acidification of streams have been viewed as important causes of the mass mortality events in FPM. However, in many of these investigations, possible infections from protist parasites were never considered. Here report on a novel parasite associated with several population losses in Swedish rivers. Phylogenetic analysis of the first molecular data for this parasite (18S rDNA gene) revealed that it is related to a terrestrial group of gregarines (Apicomplexa), specifically to parasites of tadpoles belonging to the genus Nematopsis. Further investigations of environmental data revealed the presence of this parasite in Canadian peat bogs and Swedish lakes. We describe the parasite using histology, in-situ hybridization, and transmission electron microscopy and propose a tentative life cycle within the FPM host. Together, our results identify for the first time a pathogenic agent that maybe responsible for the steady decline of a critical animal species in freshwater ecosystems worldwide.
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| 4. |
- Alfjorden, Anders, et al.
(författare)
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Identification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (Margaritifera margaritifera) in Sweden
- 2024
-
Ingår i: JOURNAL OF EUKARYOTIC MICROBIOLOGY. - 1066-5234 .- 1550-7408.
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Tidskriftsartikel (refereegranskat)abstract
- Freshwater bivalves play key ecological roles in lakes and rivers, largely contributing to healthy ecosystems. The freshwater pearl mussel, Margaritifera margaritifera, is found in Europe and on the East coast of North America. Once common in oxygenated streams, M. margaritifera is rapidly declining and consequently assessed as a threatened species worldwide. Deterioration of water quality has been considered the main factor for the mass mortality events affecting this species. Yet, the role of parasitic infections has not been investigated. Here, we report the discovery of three novel protist lineages found in Swedish populations of M. margaritifera belonging to one of the terrestrial groups of gregarines (Eugregarinorida, Apicomplexa). These lineages are closely related-but clearly separated-from the tadpole parasite Nematopsis temporariae. In one lineage, which is specifically associated with mortality events of M. margaritifera, we found cysts containing single vermiform zoites in the gills and other organs of diseased individuals using microscopy and in situ hybridization. This represents the first report of a parasitic infection in M. margaritifera that may be linked to the decline of this mussel species. We propose a tentative life cycle with the distribution of different developmental stages and potential exit from the host into the environment.
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| 5. |
- Bass, David, et al.
(författare)
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Ascetosporea
- 2019
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Ingår i: Current Biology. - : CELL PRESS. - 0960-9822 .- 1879-0445. ; 29:1, s. R7-R8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
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| 7. |
- Burki, Fabien, et al.
(författare)
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Diversity and ecology of protists revealed by metabarcoding
- 2021
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Ingår i: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 31:19, s. R1267-R1280
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Forskningsöversikt (refereegranskat)abstract
- Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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| 8. |
- Burki, Fabien
(författare)
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Mitochondrial Evolution : Going, Going, Gone
- 2016
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 26:10, s. R410-R412
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 9. |
- Burki, Fabien
(författare)
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The Convoluted Evolution of Eukaryotes With Complex Plastids
- 2017
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Ingår i: Secondary Endosymbioses. - : Elsevier. - 9780128026519 ; , s. 1-30
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 10. |
- Burki, Fabien, et al.
(författare)
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The New Tree of Eukaryotes
- 2020
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Ingår i: Trends in Ecology & Evolution. - : ELSEVIER SCIENCE LONDON. - 0169-5347 .- 1872-8383. ; 35:1, s. 43-55
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Forskningsöversikt (refereegranskat)abstract
- For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels.
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| 11. |
- Curtis, Bruce A., et al.
(författare)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 12. |
- Hehenberger, Elisabeth, et al.
(författare)
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Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont
- 2016
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 33:9, s. 2376-2390
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Tidskriftsartikel (refereegranskat)abstract
- While we know much about the evolutionary patterns of endosymbiotic organelle origins, we know less about how the actual process unfolded within each system. This is partly due to the massive changes endosymbiosis appears to trigger, and partly because most organelles evolved in the distant past. The dinotoms are dinoflagellates with diatom endosymbionts, and they represent a relatively recent but nevertheless obligate endosymbiotic association. We have carried out deep sequencing of both the host and endosymbiont transcriptomes from two dinotoms, Durinskia baltica and Glenodinium foliaceum, to examine how the nucleocytosolic compartments have functionally integrated. This analysis showed little or no functional reduction in either the endosymbiont or host, and no evidence for genetic integration. Rather, host and endosymbiont seem to be bound to each other via metabolites, such as photosynthate exported from the endosymbiont to the host as indicated by the presence of plastidic phosphate translocators in the host transcriptome. The host is able to synthesize starch, using plant-specific starch synthases, as a way to store imported photosynthate.
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| 13. |
- Hocke, Emma Filtenborg, et al.
(författare)
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Unravelling the Phylogeny of a Common Intestinal Protist : intrageneric Diversity of Endolimax
- 2022
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Ingår i: Protist. - : Elsevier. - 1434-4610 .- 1618-0941. ; 173:5
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Tidskriftsartikel (refereegranskat)abstract
- Endolimax nana is a common endobiont of the human intestine, but members of the genus have also been reported in non-human hosts and in non-intestinal organs. Limited information is available regarding the genetic diversity of Endolimax , which is necessary to delineate species, host specificity and potential differences in clinical impact on the host. Here, we used cloning of PCR products fol-lowed by Sanger sequencing and next-generation PacBio Sequencing to obtain Endolimax-related nuclear ribosomal gene sequences and undertook a phylogenetic analysis to gain additional insight into the taxonomy of Endolimax and related organisms. The new sequences confirmed that E. nana forms a discrete clade within the Archamoebae and is related to Endolimax piscium and Iodamoeba. However, we identified substantial sequence divergence within E. nana and evidence for two distinct clades, which we propose to name E. nana ribosomal lineage 1 and E. nana ribosomal lineage 2. Both of the sequencing approaches applied in the study helped us to improve our understanding of genetic diversity across Endolimax , and it is likely that wider application of next-generation sequencing tech-nologies will facilitate the generation of Endolimax-related DNA sequence data and help complete our understanding of its phylogenetic position and intrageneric diversity.
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| 14. |
- Irisarri, Iker, 1984-, et al.
(författare)
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Phylogenomic Insights into the Origin of Primary Plastids
- 2021
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 71:1, s. 105-120
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Tidskriftsartikel (refereegranskat)abstract
- The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and nonmonophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the monophyly of Archaeplastida hosts in four available phylogenomic data sets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes were investigated. Our analyses revealed a lack of support for host monophyly in the shorter individual data sets. However, when analyzed together under rigorous data curation and complex mixture models, the combined nuclear data sets supported the monophyly of primary photosynthetic eukaryotes (Archaeplastida) and recovered a putative association with plastid-lacking Picozoa. This study represents an important step toward better understanding deep eukaryotic evolution and the origin of plastids.
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| 15. |
- Irwin, Nicholas, et al.
(författare)
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Phylogenomics supports the monophyly of the Cercozoa
- 2019
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 130, s. 416-423
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 16. |
- Jamy, Mahwash
(författare)
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Environmental sequencing to infer patterns of eukaryotic evolution : Combining long-read and short-read metabarcoding
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Our view of eukaryotes is biased towards plants, animals, and fungi. But the vast majority of eukaryotic diversity is microbial in nature. These microbial eukaryotes are key players in all ecosystems on earth and are collectively known as protists. Over the past decade we have gathered a better understanding of environmental protist diversity and ecology through metabarcoding studies, which routinely generate millions of reads corresponding to short fragments (< 500 bp) of the 18S gene. However, the limited phylogenetic signal of these short reads hinders their use in investigating questions of an evolutionary nature. To overcome this limitation, we introduced a method for long-read metabarcoding in Paper I of this thesis. We validated this method by amplifying DNA from three soil samples and sequencing with PacBio to obtain a ca. 4500 bp region of the ribosomal DNA operon spanning the 18S and 28S genes. The long-reads were taxonomically annotated using a phylogeny-aware approach, and were used to infer robust 18S-28S phylogenies of the environmental diversity. In Paper II, we investigated habitat evolution across the eukaryotic tree of life, using a unique combination of long-read and short-read metabarcoding data in a phylogenetic framework. We showed that transitions across the marine-terrestrial habitat boundary are more frequent than previously assumed, and that eukaryotic groups vary in their ability to cross this habitat boundary. We inferred that the last eukaryotic common ancestor inhabited non-marine environments, and that subsequent transitions across the marine-terrestrial boundary likely played a key role in eukaryotic evolution by opening new niches to fill.Paper III focused on determining the effects of habitat and latitude on the rates of molecular evolution of protists. Analyses on phylogenies inferred from long-read metabarcoding data found no systematic differences in the evolutionary rates of marine and terrestrial species. Additionally, contrary to expectations, not all eukaryotic groups showed an increase in evolutionary rates towards the equator, with some groups displaying the opposite trend. Finally Paper IV isolates the parasite of the endangered freshwater pearl mussel in Sweden, and phylogenetic analyses including long-read metabarcoding data identifies it as a gregarine belonging to the genus Nematopsis. In summary, this thesis introduces a new method for environmental sequencing of protists, and urges future studies to use both long-read and short-read metabarcoding data to study outstanding questions in eukaryotic evolution and ecology.
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| 17. |
- Jamy, Mahwash, et al.
(författare)
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Global patterns and rates of habitat transitions across the eukaryotic tree of life
- 2022
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Ingår i: Nature Ecology & Evolution. - : Springer Nature. - 2397-334X. ; 6:10, s. 1458-1470
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Tidskriftsartikel (refereegranskat)abstract
- The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.
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| 18. |
- Jamy, Mahwash, et al.
(författare)
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Habitat, latitude, and the rate of molecular evolution in microbial eukaryotes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Numerous studies over the years have found that molecular evolution does not progress in a constant, clock-like manner. Instead, evolutionary rates show complex patterns and can vary even between closely related species. Studying the underlying causes of these rate variations is important to improve our understanding of evolutionary processes. In this study, we investigate how majors habitat types (marine or terrestrial) and geography (latitude) can impact the rate of molecular evolution across the tree of eukaryotes, using long-read and short-read metabarcoding data placed in a phylogenetic framework. We did not find any systematic differences in the rate of evolution between marine and terrestrial species. However found a weak association between habitat colonization and increased rates of evolution. Evolutionary rates are expected to be higher in the tropics due to higher temperature, however we observed this pattern for only a few groups of marine protists. Several protist groups displayed no impact of latitude on rates of evolution, while some instead showed an inverse trend. These results cast doubt on the generality of the “kinetic energy hypothesis” which proposes a link between latitude/temperature and rates of molecular evolution.
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| 19. |
- Jamy, Mahwash, et al.
(författare)
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Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
- 2020
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 20:2, s. 429-443
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long-read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain an 4500-bp region spanning most of the eukaryotic small subunit (18S) and large subunit (28S) ribosomal DNA genes. We first treated the CCS reads with a novel curation workflow, generating 650 high-quality operational taxonomic units (OTUs) containing the physically linked 18S and 28S regions. To assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based methods. The taxonomically annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing us to accurately derive the evolutionary origin of environmental diversity. A total of 1,019 sequences were included, of which a majority (58%) corresponded to the new long environmental OTUs. The long reads also allowed us to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Together, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.
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| 20. |
- Janouskovec, Jan, et al.
(författare)
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A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction
- 2017
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 27:23, s. 3717-3724.e5
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 21. |
- Janouškovec, Jan, et al.
(författare)
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Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:2, s. E171-E180
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 22. |
- Keeling, Patrick J., et al.
(författare)
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Progress towards the Tree of Eukaryotes
- 2019
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Ingår i: Current Biology. - : CELL PRESS. - 0960-9822 .- 1879-0445. ; 29:16, s. R808-R817
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 23. |
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| 24. |
- Onuţ-Brännström, Ioana, et al.
(författare)
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A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea)
- 2023
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 15:3
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Tidskriftsartikel (refereegranskat)abstract
- Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron–sulfur cluster (ISC) pathway-mediated Fe–S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.
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| 25. |
- Santoferrara, Luciana, et al.
(författare)
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Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding
- 2020
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Ingår i: Journal of Eukaryotic Microbiology. - : WILEY. - 1066-5234 .- 1550-7408. ; 67:5, s. 612-622
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Tidskriftsartikel (refereegranskat)abstract
- During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on shortDNAsequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding.
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| 26. |
- Schön, Max Emil, 1990-
(författare)
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Evolutionary transitions across the tree of life : Phylogenomic case studies in environmental archaea, bacteria and eukaryotes
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microbes form the majority of life on Earth, but have been systematically underrepresented in historical research. The sequencing revolutions of the last two decades have completely changed the way we can study microbial genomic information, giving us the means to probe ever deeper into their evolution. In a first study, we developed a new approach to screen large short-read datasets for the presence of lineages and genes of interest. By using gene-centric assembly and phylogenetic placement, we integrate the strengths of reference-based with phylogenetic screening methods to efficiently reconstruct gene sequences and label them taxonomically. This will enable researchers to more efficiently select datasets which are likely to contain desired lineages and genes.In the second study, we recover five metagenome-assembled genomes from the previously uncharacterized Hikarchaeia. We infer them to be the closest relatives of haloarchaea and study the evolution of genome content since the last common ancestor of these two aerobic groups with anaerobic methanogens. We detect patterns of gradual evolutionary transition, including the early loss of methanogenesis-related genes and the acquisition of the genetic basis for aerobic respiration. Furthermore, genomes of haloarchaea underwent significant expansion, mostly through transfers from diverse groups of bacteria, whereas Hikarchaeia display genome streamlining typical of marine prokaryotes.In a third study, we reconstructed two new bacterial families, Mitibacteraceae and Athabascaceae, that branch as sister clades to all previously known Rickettsiales. Their genomes lack the characteristic reduction of rickettsial bacteria but resemble free-living alphaproteobacteria. However, they contain several conserved features, such as the rvh type 4 secretion system. We reconstructed the last common ancestor of all Rickettsiales and inferred it as a free-living organism associated with marine biofilms. Further, we propose a model for the transition towards host-association found in all classical Rickettsiales.The fourth study explores the diversity and evolution of the eukaryotic orphan lineage Picozoa. With the help of 43 new single amplified genomes, Picozoa are placed within the supergroup Archaeplastida, in a clade together with red algae and the predatory rhodelphids. In contrast to other archaeplastids, picozoan genomes show no sign of a (cryptic) plastid or plastid-associated gene transfers. This suggests that Picozoa completely lost the primary plastid early in their evolution, or that in fact they never possessed it. These findings raise further questions about the acquisition of the plastid in the archaeplastidal ancestor and the frequency of plastid loss.In summary, this thesis explores several important evolutionary transitions across the tree of life using environmental genome reconstruction, phylogenomics and ancestral state reconstruction approaches.
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| 27. |
- Schön, Max Emil, et al.
(författare)
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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we used single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.
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| 28. |
- Strassert, Jürgen F. H., et al.
(författare)
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A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth. There are several competing hypotheses for the acquisition of red algal-derived plastids by eukaryotic phytoplankton. Here, the authors use Bayesian molecular clock analyses to evaluate the chronological possibility of the proposed plastid origins and transmissions.
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| 29. |
- Strassert, Jürgen F. H., et al.
(författare)
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New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
- 2019
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Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 36:4, s. 757-765
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 30. |
- Strassert, Jürgen F H, et al.
(författare)
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Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates
- 2018
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Ingår i: The ISME Journal. - : Macmillan Publishers Ltd.. - 1751-7362 .- 1751-7370. ; 12, s. 304-308
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 31. |
- Sørensen, Megan E. S., et al.
(författare)
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A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration
- 2023
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 33:17, s. 3571-3584, e1-e6
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Tidskriftsartikel (refereegranskat)abstract
- Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems and for understanding the evolution of plastids. Kleptoplastidy, where the plastids of prey are temporarily retained and continuously re-acquired, provides opportunities to study the transitional states of plastid establishment. Here, we investigated the poorly studied marine centrohelid Meringosphaera and its previously unidentified symbionts using culture-independent methods from environmental samples. Investigations of the 18S rDNA from single-cell assembled genomes (SAGs) revealed uncharacterized genetic diversity within Meringosphaera that likely represents multiple species. We found that Meringosphaera harbors plastids of Dictyochophyceae origin (stramenopiles), for which we recovered six full plastid genomes and found evidence of two distinct subgroups that are congruent with host identity. Environmental monitoring by qPCR and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) revealed seasonal dynamics of both host and plastid. In particular, we did not detect the plastids for 6 months of the year, which, combined with the lack of plastids in some SAGs, suggests that the plastids are temporary and the relationship is kleptoplastidic. Importantly, we found evidence of genetic integration of the kleptoplasts as we identified host-encoded plastid-associated genes, with evolutionary origins likely from the plastid source as well as from other alga sources. This is only the second case where host-encoded kleptoplast-targeted genes have been predicted in an ancestrally plastid-lacking group. Our results provide evidence for gene transfers and protein re-targeting as relatively early events in the evolution of plastid symbioses.
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| 32. |
- Tice, Alexander K., et al.
(författare)
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PhyloFisher : A phylogenomic package for resolving eukaryotic relationships
- 2021
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 19:8
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic "single-copy orthogroup" datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.
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| 33. |
- Tikhonenkov, Denis, V, et al.
(författare)
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On the origin of TSAR : morphology, diversity and phylogeny of Telonemia
- 2022
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Ingår i: Open Biology. - : The Royal Society. - 2046-2441. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Telonemia is a poorly known major phylum of flagellated eukaryotes with a unique combination of morphological traits. Phylogenomics recently revealed the phylogenetic position of telonemids as sister to SAR, one of the largest groups of eukaryotes, comprising Stramenopiles, Alveolata and Rhizaria. Due to this key evolutionary position, investigations of telonemids are of critical importance for elucidating the origin and diversification of an astounding diversity of eukaryotic forms and life strategies. To date, however, only two species have been morphologically characterized from Telonemia, which do not represent this genetically very diverse group. In this study, we established cultures for six new telonemid strains, including the description of five new species and a new genus. We used these cultures to update the phylogeny of Telonemia and provide a detailed morphological and ultrastructural investigation. Our data elucidate the origin of TSAR from flagellates with complex morphology and reconstruction of the ancestral structure of stramenopiles, alveolates and rhizarians, and their main synapomorphic characters. Since telonemids are a common component of aquatic environments, the features of their feeding, behaviour and ecological preferences observed in clonal cultures and the results of global metabarcoding analysis contribute to a deeper understanding of organization of microbial food webs.
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| 34. |
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| 35. |
- Whelan, Simon, et al.
(författare)
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PREQUAL : detecting non-homologous characters in sets of unaligned homologous sequences
- 2018
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Ingår i: Bioinformatics. - : OXFORD UNIV PRESS. - 1367-4803 .- 1367-4811. ; 34:22, s. 3929-3930
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Tidskriftsartikel (refereegranskat)abstract
- 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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| 36. |
- Xiao, Linhong, et al.
(författare)
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Photophysiological response of Symbiodiniaceae single cells to temperature stress
- 2022
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Ingår i: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 16:8, s. 2060-2064
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic dinoflagellates in the family Symbiodiniaceae engage in symbiosis with scleractinian corals. As coral ‘bleaching’ is partly governed by the thermal sensitivity of different Symbiodiniaceae lineages, numerous studies have investigated their temperature sensitivity. However, the systematic identification of single-cells with increased temperature resistance among these dinoflagellates has remained inaccessible, mostly due to a lack of technologies operating at the microscale. Here, we employed a unique combination of microfluidics, miniaturized temperature control, and chlorophyll fluorometry to characterize the single-cell heterogeneity among five representative species within the Symbiodiniaceae family under temperature stress. We monitored single-cell maximum quantum yields (Fv/Fm) of photosystem (PS) II under increasing temperature stress (22‒39 °C, + 1 °C every 15 min), and detected a significant Fv/Fm reduction at lineage-specific temperatures ranging from 28 °C to 34 °C alongside a 40- to 180- fold increase in intraspecific heterogeneity under elevated temperatures (>31 °C). We discovered that the initial Fv/Fm of a cell could predict the same cell’s ability to perform PSII photochemistry under moderate temperature stress (<32 °C), suggesting its use as a proxy for measuring the thermal sensitivity among Symbiodiniaceae. In combination, our study highlights the heterogeneous thermal sensitivity among photosynthetic Symbiodiniaceae and adds critical resolution to our understanding of temperature-induced coral bleaching.
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| 37. |
- Zarsky, Vojtech, et al.
(författare)
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Contrasting outcomes of genome reduction in mikrocytids and microsporidians
- 2023
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Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 21
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution.Results: At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths.Conclusions: Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.
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| 38. |
- Zlatogursky, Vasily V., et al.
(författare)
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The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan
- 2021
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Ingår i: Journal of Eukaryotic Microbiology. - : John Wiley & Sons. - 1066-5234 .- 1550-7408. ; 68:5
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Tidskriftsartikel (refereegranskat)abstract
- Meringosphaera is an enigmatic marine protist without clear phylogenetic affiliation, but it has long been suggested to be a chrysophyte-related autotroph. Microscopy-based reports indicate that it has a worldwide distribution, but no sequence data exist so far. We obtained the first 18S rDNA sequence for M. mediterranea (identified using light and electron microscopy) from the west coast of Sweden. Observations of living cells revealed granulated axopodia and up to 6 globular photosynthesizing bodies about 2 mu m in diameter, the nature of which requires further investigation. The ultrastructure of barbed undulating spine scales and patternless plate scales with a central thickening is in agreement with previous reports. Molecular phylogenetic analysis placed M. mediterranea inside the NC5 environmental clade of Centroplasthelida (Haptista) along with additional environmental sequences, together closely related to Choanocystidae. This placement is supported by similar scales in Meringosphaera and Choanocystidae. We searched the Tara Oceans 18S V9 metabarcoding dataset, which revealed four OTUs with 94.8%-98.2% similarity, with oceanic distribution similar to that based on morphological observations. The current taxonomic position and species composition of the genus are discussed. The planktonic lifestyle of M. mediterranea contradicts the view of some authors that centrohelids enter the plankton only temporarily.
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