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Genomics and Evolution of Eukaryotic Microorganisms

Research topics

Our research concerns the diversity, ecology and evolution of eukaryotic microorganisms. We are interested in the matter of the eukaryotic cell’s evolution, including the evolution of organella of endosymbiotic origin, as well as the effect of horizontal gene transfer (HGT) on the evolution of Eukaryota. The study of genomes and transcriptomes of eukaryotic microorganisms allow to find answers regarding the early stages of endosymbiosis, evolution of organellar genomes and the reductive evolution of organella. We also strive to understand the role of eukaryotic microorganisms in water habitats through researching their diversity and metabolic potential as well as their interactions with other microorganisms.

Our work consists of both traditional methods of cell culture and isolation as well as basic molecular biology approach. However, we mostly focus on utilising the potential of Next Generation Sequencing (NGS) and bioinformatical analysis. We work with genome, transcriptome, metagenome and amplicon sequencing data. We also develop original bioinformatic tools adapted to data derived from Eukaryota.


Establishing the protocol for high-throughput single-cell transcriptomics of microbial eukaryotes, New Ideas, Excellence Initiative Research University

Photosymbiosis in freshwater ciliates: elucidating its diversity, functioning and evolution with single-cell sequencing, Preludium BIS Grant, National Science Centre

Structure and evolution of mitochondrial genomes in Euglenids, Preludium Grant, National Science Centre

Monitoring diversity of microbial dark matter in expanding anoxic zones, Charles University 4EU+ minigrant

Freshwater microbial communities in the eutrophication gradient: diversity and interactions of protists and bacteria (MicroDivEr), Opus Grant, National Science Centre

Evolution of photorophy in Eukaryotes, EMBO Installation Grant

Evolution and function of the inverted repeats (IR) in plastid genomes of Euglenophyta, Preludium Grant, National Science Centre Poland


Publications review

Karlicki, Michał; Antonowicz, Stanisław; Karnkowska, Anna

Tiara: deep learning-based classification system for eukaryotic sequences Journal Article

Bioinformatics, 38 (2), pp. 344–350, 2022.

Abstract | Links | BibTeX

Maciszewski, Kacper; Dabbagh, Nadja; Preisfeld, Angelika; Karnkowska, Anna

Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes Journal Article

Molecular Phylogenetics and Evolution, 170 , pp. 107441, 2022, ISSN: 1055-7903.

Abstract | Links | BibTeX

Treitli, Sebastian Cristian; Peña-Diaz, Priscila; Hałakuc, Paweł; Karnkowska, Anna; Hampl, Vladimír

High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis Journal Article

Microbial Genomics, 7 (12), pp. 000745, 2021, ISSN: 2057-5858.

Abstract | Links | BibTeX

Kostygov, Alexei Y; Karnkowska, Anna; Votypka, Jan; Tashyreva, Daria; Maciszewski, Kacper; Yurchenko, Vyacheslav; Lukes, Julius

Euglenozoa : taxonomy, diversity and ecology, symbioses and viruses Journal Article

Open Biology, 11 (3), pp. 200407-200407, 2021, ISBN: 0000000337.

Abstract | Links | BibTeX

Kayama, Motoki; Maciszewski, Kacper; Yabuki, Akinori; Miyashita, Hideaki; Karnkowska, Anna; Kamikawa, Ryoma

Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis. Journal Article

Frontiers in Plant Science, 11 , pp. 1859 , 2020.

Links | BibTeX

Lukešová, Soňa; Karlicki, Michał; Hadariová, Lucia Tomečková; Szabová, Jana; Karnkowska, Anna; Hampl, Vladimír

Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments Journal Article

Environmental Microbiology Reports, 12 (1), pp. 78-91, 2020.

Abstract | Links | BibTeX

Jagielski, Tomasz; Bakuła, Zofia; Gawor, Jan; Maciszewski, Kacper; Kusber, Wolf-Henning; Dyląg, Mariusz; Nowakowska, Julita; Gromadka, Robert; Karnkowska, Anna

The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies Journal Article

Algal Research, 43 , pp. 101639, 2019, ISSN: 2211-9264.

Abstract | Links | BibTeX

Maciszewski, Kacper; Karnkowska, Anna

Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles Journal Article

Current Opinion in Genetics & Development, 58-59 , pp. 33-39, 2019, ISSN: 0959-437X, (Evolutionary genetics).

Abstract | Links | BibTeX

Han, Kwi Young; Maciszewski, Kacper; Graf, Louis; Yang, Ji Hyun; Andersen, Robert A; Karnkowska, Anna; Yoon, Hwan Su

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization Journal Article

Journal of Phycology, 55 (5), pp. 1166-1180, 2019.

Abstract | Links | BibTeX

Karnkowska, Anna; Treitli, Sebastian C; Brzoň, Ondřej; Novák, Lukáš; Vacek, Vojtěch; Soukal, Petr; Barlow, Lael D; Herman, Emily K; Pipaliya, Shweta V; Pánek, Tomáš; Žihala, David; Petrželková, Romana; Butenko, Anzhelika; Eme, Laura; Stairs, Courtney W; Roger, Andrew J; Eliáš, Marek; Dacks, Joel B; Hampl, Vladimír

The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Journal Article

Molecular Biology and Evolution, 36 (10), pp. 2292-2312, 2019, ISSN: 0737-4038.

Abstract | Links | BibTeX

Karnkowska, Anna; Bennett, Matthew S; Triemer, Richard E

Dynamic evolution of inverted repeats in Euglenophyta plastid genomes Journal Article

Scientific Reports, 8 (1), pp. 16071, 2018, ISSN: 2045-2322.

Abstract | Links | BibTeX

Jagielski, Tomasz; Gawor, Jan; Bakuła, Zofia; Decewicz, Przemysław; Maciszewski, Kacper; Karnkowska, Anna

cytb as a New Genetic Marker for Differentiation of Prototheca Species Journal Article

Journal of Clinical Microbiology, 56 (10), 2018, ISSN: 0095-1137.

Abstract | Links | BibTeX

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