| 1. |
- 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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| 2. |
- Florenza, Javier
(författare)
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Single-cell methodologies for ecological and metabolic mapping of mixotrophic microeukaryotes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mixotrophy in aquatic protists is pivotal for our understanding of aquatic microbial food web dynamics. This thesis is centered around aquatic unicellular mixotrophs, and comprises three methodological approaches aimed to tackle mixotroph ecology at single-cell resolution: the identification of actively feeding mixotrophs in natural samples, the determination of specific interactions among mixotrophs and bacterial prey, and the profiling of two distinct mixotrophic populations based on the gene expression of their constitutive individuals.First, we investigated the feasibility of cytometrically sorting actively feeding mixotrophs from a natural community. The approach was based on the use of fluorescently labelled feeding tracers (FLTs) in conjunction with chloroplast autofluorescence from the feeding cell to retrieve mixotrophic individuals for subsequent single cell characterization by sequencing of a taxonomic marker gene. The preference for different FLT types showed that for mixotrophs in culture, FLT size was the strongest factor influencing FLT-based capture. This approach was then used to identify actively feeding mixotrophs from a lake water sample. The method proved to be both highly selective and specific and allowed the identification of an active natural mixotrophic community of unexpected diversity.Secondly, we explored the potential of adapting emulsion, paired-isolation and concatenation PCR (epicPCR) to uncover physical connections between individual unicellular eukaryotes and their associated bacterial cohort. The results from three proof-of-concept experiments, however, did not conform to the expectations and showcased several deficiencies that need to be addressed. Mainly, the frequency of recovered links showed that the protocol, as deployed in our experiments, was prone to yield spurious abundance-driven associations between the eukaryotes and bacteria, since the most abundant bacteria were the ones driving the strongest associations with our test predators. Nevertheless, we identify possible solutions and point to avenues for future development to overcome the current limitations.Finally, the capability of full-transcript single-cell RNA sequencing was surveyed to provide a reliable transcriptomic landscape of a non-mammalian, non-model eukaryotic organism with no available reference genome. We could show that, while some of the detailed functional information might remain uncharacterized, the workflow provide sufficient raw data to resolve population structure based on expression profiles.In summary, with varying degrees of success, these attempts to expose and study mixotrophic unicellular eukaryotes demonstrate that the time is ripe to explore the ecology of mixotrophs at single-cell level.
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| 3. |
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| 4. |
- 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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| 5. |
- Strassert, Jürgen F. H., et al.
(författare)
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Phylogeny, Evidence for a Cryptic Plastid, and Distribution of Chytriodinium Parasites (Dinophyceae) Infecting Copepods
- 2019
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Ingår i: Journal of Eukaryotic Microbiology. - : Wiley. - 1066-5234 .- 1550-7408. ; 66:4, s. 574-581
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Tidskriftsartikel (refereegranskat)abstract
- Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium, which seemed to be attached to a copepod nauplius, to analyze the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.
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| 6. |
- 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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