Anna Karnkowska

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Verified

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• PhD
• Associate Professor at University of Warsaw

The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. Here, we report the genome sequence of a microbial eukaryote, the oxymonad Monocercomonoides sp., which revealed that this organism lacks all hallmark mitochondrial proteins. Crucially, the mitochondr...

Motivation With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step towards a better understanding of eukaryotic diversity. Results We developed Tiara, a deep-learning-based approach for the identif...

Kleptoplasts are distinct among photosynthetic organelles in eukaryotes (i.e, plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza...

Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecos...

Though endosymbioses between protists and prokaryotes are widespread, certain host lineages have received disproportionate attention what may indicate either a predisposition to such interactions or limited studies on certain protist groups due to lack of cultures. The euglenids represent one such group in spite of microscopic observations showing...

Relacje symbiotyczne jednokomórkowych eukariontów (protistów) odegrały kluczową rolę w powstaniu i różnicowaniu organizmów eukariotycznych. Mają też duże znaczenie dla funkcjonowania ekosystemów, a mimo to pozostają nadal dość słabo zbadane. Mikroorganizmy eukariotyczne wchodzą w relacje symbiotyczne zarówno jako gospodarze, jak i symbionty. Mogą t...

Background Plastids are usually involved in photosynthesis, but the secondary loss of this function is a widespread phenomenon in various lineages of algae and plants. In addition to the loss of genes associated with photosynthesis, the plastid genomes of colorless algae are frequently reduced further. To understand the pathways of reductive evolut...

The origin of eukaryotic cells is a key milestone in life’s history on Earth.

Historia komórki eukariotycznej.

The mito-metagenomics (MMG) approach inovolves directly sequencing pooled samples, yields numerous mitochondrial reads that can be assembled into full or partial mitogenomes. This method circumvents the challenges associated with PCR-based metabarcoding and hold significant promise in biodiversity and phylogeny study. However, a reference database...

Plastids are endosymbiotic organelles widespread among eukaryotic lineages. They were pivotal in the evolution of eukaryotes, as they allowed host eukaryotic cells to perform photosynthesis. From an evolutionary point of view, there are two main types of plastids, primary and complex (higher-order) plastids. Primary plastids originated through a si...

Plastids are usually involved in photosynthesis, but the secondary loss of this function is a widespread phenomenon in various lineages of algae and plants. In addition to the loss of genes associated with photosynthesis, the plastid genomes of colorless algae are frequently reduced further. To understand the pathways of reductive evolution associa...

Microbial communities, consisting of prokaryotes and protists, play a central role in ecological processes in aquatic environments. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and to track spatio-temporal dynamics in both marine and freshwater environments. While previous research ha...

The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in...

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 nucle...

Most Parabasalia are symbionts in the hindgut of "lower" (non-Termitidae) termites, where they widely vary in morphology and degree of morphological complexity. Large and complex cells in the class Cristamonadea evolved by replicating a fundamental unit, the karyomastigont, in various ways. We describe here four new species of Calonymphidae (Crista...

The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence‐structure data are encod...

Kleptoplasts are distinct among photosynthetic organelles in eukaryotes (i.e, plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza...

Background Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal...

The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis , the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed i...

Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional so...

Plastids, similarly to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations come...

Plastids, similarly to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations come...

Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of t...

Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plas...

teaserEuglenoids show great promise to benefit our world; as biofuels, environmental remediators, anti-cancer agents, robotics design simulators and food nutritional agents, but the absence of reference genomes currently limit realizing these benefits. The Euglena International Network (EIN) (https://euglenanetwork.org/) aims to address these chall...

Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented...

Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of t...

Background: Memebers of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal tr...

Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plas...

Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting ge...

Cristamonadea is a large class of parabasalian protists that reside in the hindguts of wood-feeding insects, where they play an essential role in the digestion of lignocellulose. This group of symbionts boasts an impressive array of complex morphological characteristics, many of which have evolved multiple times independently. However, their divers...

Euglenozoa is a species-rich group of protists, which have extremely diverse lifestyles and a range of features that distinguish them from other eukar-yotes. They are composed of free-living and parasitic kinetoplastids, mostly free-living diplonemids, heterotrophic and photosynthetic euglenids, as well as deep-sea symbiontids. Although they form a...

Motivation: With a large number of metagenomic datasets becoming available, the eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step towards the better understanding of eukaryotic diversity. Results: We developed Tiara, a deep-learning-based approach for iden...

Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are al...

Organisms that have lost their photosynthetic capabilities are present in a variety of eukaryotic lineages, such as plants and disparate algal groups. Most of such non-photosynthetic eukaryotes still carry plastids, as these organelles retain essential biological functions. Most non-photosynthetic plastids possess genomes with varied protein-coding...

Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting ge...

The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available...

Of the Prototheca genus, Prototheca wickerhamii has the highest clinical significance in humans. However, neither nuclear nor organellar genomes of this species were sequenced until now. The hitherto determined and analyzed mitochondrial and plastid genomes of the alleged P. wickerhamii species belong in fact to another species, recently named Prot...

Several eukaryotic lineages gained the ability of photosynthesis by acquiring plastids in the events of primary endosymbiosis with cyanobacteria, or secondary endosymbiosis with plastid-bearing eukaryotes. Plastids possess genomes (ptDNA) with genetic contents considerably reduced as a result of gene losses and transfers to the host’s nucleus. Stil...

Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relati...

Our knowledge on the variability of the reduced forms of endosymbiotic organelles – mitochondria and plastids – is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in un...

The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here we report an extensive analysis of the...

The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here we report an extensive analysis of the...

Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here we present the first co...

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 ye...

Photosynthetic euglenids (Euglenophyta) are a monophyletic group of unicellular eukaryotes characterized by the presence of plastids, which arose as the result of the secondary endosymbiosis. Many Euglenophyta plastid (pt) genomes have been characterized recently, but they represented mainly one family – Euglenaceae. Here, we report a comparative a...

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...

Achlorophyllous unicellular microalgae of the genus Prototheca (Trebouxiophyceae, Chlorophyta) are the only known plants that cause infections in both humans and animals, collectively referred to as protothecosis. Human protothecosis, most commonly manifested as cutaneous, articular, and disseminated disease, is primarily caused by P. wickerhamii ,...

Pseudotrichonympha is a large and structurally complex genus of parabasalian protists that play a key role in the digestion of lignocellulose in the termite hindgut. Like many termite symbionts, it has a conspicuous body plan that makes genus-level identification relatively easy, but species-level diversity of Pseudotrichonympha is understudied. Mo...

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 geno...

Euglenids are a group of >1500 described species of single-celled flagellates with diverse modes of nutrition, including phagotrophy and photoautotrophy. The group also encompasses a clade of specialist “primary” osmotrophs (Aphagea) and, very likely, one group of phagotrophs that are ectosymbiont-supporting anaerobes (Symbiontida). Almost all eugl...

Members of the genus Trichonympha are among the most well-known, recognizable and widely distributed parabasalian symbionts of lower termites and the wood-eating cockroach species of the genus Cryptocercus. Nevertheless, the species diversity of this genus is largely unknown. Molecular data have shown that the superficial morphological similarities...

Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and...

Euglenids are a group of >1500 described species of single-celled flagellates with diverse modes of nutrition, including phagotrophy and photoautotrophy. The group also encompasses a clade of specialist “primary” osmotrophs (Aphagea) and, very likely, one group of phagotrophs that are ectosymbiont-supporting anaerobes (Symbiontida). Almost all eugl...

The concept of a phylogeny of parasites is inextricably linked to that of the phylogeny of eukaryotes. Though it can be useful to infer functional principles from similar morphologies and trophic strategies, the evolutionary histories of parasites are most accurately viewed as independent shifts to this lifestyle from a free-living state. This chap...

Background Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the comp...

Due to their involvement in the energy metabolism, mitochondria are essential for most eukaryotic cells. Microbial eukaryotes living in low oxygen environments possess reduced forms of mitochondria, namely mitochondrion-related organelles (MROs). These do not produce ATP by oxidative phosphorylation on their membranes and some do not produce ATP at...

Autotrophic euglenids (Euglenophyceae) are common and abundant group of microbial eukaryotes in freshwater habitats. They have a limited number of features, which can be observed using light microscopy, thus species identification is often problematic. Establishing a barcode for this group is therefore an important step towards the molecular identi...

Background: Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, whic...

Although Phacus longicauda is the type species of the genus Phacus and one of the most common species among autotrophic euglenids, its correct identification is nearly impossible. Over 30 morphologically similar taxa appear in the literature, but there are no good diagnostic features to distinguish them. Using environmental sampling and whole genom...

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions...

The microscopic Utermohl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanob...

The nuclear genomes of euglenids contain three types of introns: conventional spliceosomal introns, non-conventional introns for which a splicing mechanism is unknown (variable non-canonical borders, RNA secondary structure bringing together intron ends) and so-called intermediate introns, which combine features of conventional and non-conventional...

In this paper, we describe a new photosynthetic euglenoid species, Euglenaria clepsydroides Zakryś, sp. nov., found in Poland. A large population of this species exists in a few, small, eutrophic bodies of water inside the Masurian Landscape Park (covering a part of the Masurian Lake District in Poland). The characteristic and atypical (hourglass-l...

Euglena sanguinea (Ehrenberg 1831) was one of the first green euglenoid species described in the literature. At first, the species aroused the interest of researchers mainly due to the blood-red color of its cells, which, as it later turned out, is not a constant feature. Complicated chloroplast morphology, labeled by Pringsheim as the “peculiar ch...

Abstract The occurrence of picocyanobacteria, the smallest cell-size fraction of cyanobacteria, in low-pH waters, is still poorly studied. In this study, we tested the hypothesis that picocyanobacteria found occasionally in low-pH environments are adapted to such water conditions. We isolated picocyanobacteria by means of the cytometric method from...

The establishment of epitypes (together with the emended diagnoses) for three species of Euglenaria Karnkowska, E. W. Linton et Kwiatowski [Eu. anabaena (Mainx) Karnkowska et E. W. Linton; Eu. caudata (Hübner) Karnkowska et E. W. Linton; and Eu. clavata (Skuja) Karnkowska et E. W. Linton] and two species of Euglena Ehrenberg [E. granulata (Klebs) S...

For this study, we have examined the literature and the morphological diversity, as well as analyzed the nuclear SSU rDNA sequences of two very common and cosmopolitan species formerly known as Euglena deses Ehrenb. and Euglena intermedia (G. A. Klebs) F. Schmitz. Our studies have shown that there is evidence for distinguishing only one species (E....

The community of picocyanobacteria inhabiting the Great Mazurian Lakes system (comprising lakes ranging from mesotrophic to hypertrophic) is dominated by phycoerythrin-rich cells, which outnumber phycocyanin-rich cells, even in hypertrophic lakes. The genetic diversity and phylogeny of 43 strains of picocyanobacteria isolated from four Mazurian lak...

Using Maximum Likelihood and Bayesian analyses of three genes, nuclear SSU (nSSU) and LSU (nLSU) rDNA, and chloroplast SSU (cpSSU) rDNA, the relationships among 82 plastid-containing strains of euglenophytes were clarified. The resulting tree split into two major clades: clade one contained Euglena, Trachelomonas, Strombomonas, Colacium, Monomorphi...

The establishment of epitypes (together with emended diagnoses) for seven species of Phacus Dujardin: Phacus oscillans Klebs, Phacus parvulus Klebs, Phacus pusillus Lemmermann, Phacus skujae Skvortzov, Phacus inflexus (Kisselew) Pochmann, Phacus polytrophos Pochmann and Phacus smulkowskianus (Zakryś) Kusber was achieved thanks to literature studies...

The study showed that the picocyanobacteria community of the Great Mazurian Lakes system (GML) was dominated by phycoerythrin-rich (PE) ecotypes and demonstrated a gradual decrease of the ratio between PE and phycocyanin-rich (PC) ecotypes. The Great Mazurian Lakes offer better conditions for the PE ecotype than for the PC one, despite the consider...

Using Maximum Likelihood and Bayesian analyses of three genes, nuclear SSU (nSSU) and LSU (nLSU) rDNA, and chloroplast SSU (cpSSU) rDNA, the relationships among 82 plastid-containing strains of euglenophytes were clarified. The resulting tree split into two major clades: clade one contained Euglena, Trachelomonas, Strombomonas, Colacium, Monomorphi...

Morphological and molecular studies, as well as original literature reexamination, necessitate establishment of five Euglena species with a single axial, stellate chloroplast [Euglena viridis (O. F. Müller) Ehrenberg 1830, Euglena pseudoviridis Chadefaud 1937, Euglena stellata Mainx 1926, Euglena pseudostellata sp. nov., and Euglena cantabrica Prin...

We studied the morphological diversity and analyzed the small subunit rDNA sequences of two taxa formerly known as Euglena spirogyra Ehr. and Euglena fusca (Klebs) Lemmermann. Our studies confirmed that the two should have the rank of a species, namely Lepocinclis spirogyroides (Ehr.) Marin et Melkonian and Lepocinclis fusca (Klebs) Kosmala et Zakr...