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Evolution and Genomics of Microbial Eukaryotes

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 organelles of endosymbiotic origin, as well as the impact of horizontal gene transfer (HGT) on the evolution of Eukaryota. The study of genomes and transcriptomes of eukaryotic microorganisms allows to find answers regarding the early stages of endosymbiosis, the evolution of organellar genomes and the reductive evolution of organelles. 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 comprises cell culture, isolation methods, and molecular biology approaches. However, we mostly focus on utilising the potential of Next Generation Sequencing (NGS) and bioinformatic analysis. We work with genome, transcriptome, metagenome and amplicon sequencing data. We also develop bioinformatics tools adapted to data derived from Eukaryota.

Join our team! 

PhD position in the Sonata BIS project SYBMIOSTART! The application deadline is 3 June 2024. Read more about the project and the position here.

Projects

Unravelling the establishment of endosymbiosis: quest for intermediate evolutionary stages among microbial eukaryotes (SYMBIOSTART), Sonata BIS National Science Centre (PI: Anna Karnkowska)

Analysis of functional and taxonomic diversity of symbionts among Euglenozoa protists, Polonez BIS National Science Centre (PI: Daria Tashyreva)

Viruses of freshwater microbial eukaryotes, EMBO Solidarity Grant to Anhelina Kyrycheko

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

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

Completed projects

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

Plastid evolution and functions of colourless algae within the Euglenophytes and Dictyochophyceae, Sonata Grant, National Science Centre Poland

Collaboration

Publications review

Campo, Javier; Carlos-Oliveira, Maria; Čepička, Ivan; Hehenberger, Elisabeth; Horák, Aleš; Karnkowska, Anna; Kolisko, Martin; Lara, Enrique; Lukeš, Julius; Pánek, Tomáš; Piwosz, Kasia; Richter, Daniel J.; Škaloud, Pavel; Sutak, Robert; Tachezy, Jan; Hampl, Vladimír

The protist cultural renaissance Journal Article

In: Trends in Microbiology, 2023, ISSN: 0966-842X.

Abstract | Links | BibTeX

Novák, Lukáš V. F.; Treitli, Sebastian C.; Pyrih, Jan; Hałakuc, Paweł; Pipaliya, Shweta V.; Vacek, Vojtěch; Brzoň, Ondřej; Soukal, Petr; Eme, Laura; Dacks, Joel B.; Karnkowska, Anna; Eliáš, Marek; Hampl, Vladimír

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria Journal Article

In: PLOS Genetics, vol. 19, no. 12, pp. 1-30, 2023.

Abstract | Links | BibTeX

Hehenberger, Elisabeth; Boscaro, Vittorio; James, Erick R.; Hirakawa, Yoshihisa; Trznadel, Morelia; Mtawali, Mahara; Fiorito, Rebecca; Campo, Javier; Karnkowska, Anna; Kolisko, Martin; Irwin, Nicholas A. T.; Mathur, Varsha; Scheffrahn, Rudolf H.; Keeling, Patrick J.

New Parabasalia symbionts Snyderella spp. and Daimonympha gen. nov. from South American Rugitermes termites and the parallel evolution of a cell with a rotating “head” Journal Article

In: Journal of Eukaryotic Microbiology, vol. 70, no. 5, pp. e12987, 2023.

Abstract | Links | BibTeX

Žárský, Vojtečh; Karnkowska, Anna; Boscaro, Vittorio; Trznadel, Morelia; Whelan, Thomas A.; Hiltunen-Thorén, Markus; Onut-Brännström, Ioana; Abbott, Cathryn L.; Fast, Naomi M.; Burki, Fabien; Keeling, Patrick J.

Contrasting outcomes of genome reduction in mikrocytids and microsporidians Journal Article

In: BMC Biology, vol. 21, pp. 137, 2023.

Abstract | Links | BibTeX

Karnkowska, Anna; Yubuki, Naoji; Maruyama, Moe; Yamaguchi, Aika; Kashiyama, Yuichiro; Suzaki, Toshinobu; Keeling, Patrick J.; Hampl, Vladimír; Leander, Brian S.

Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis Journal Article

In: Proceedings of the National Academy of Sciences, vol. 120, no. 12, 2023, ISSN: 0027-8424.

Abstract | Links | BibTeX

Rackevei, A. S.; Karnkowska, A.; Wolf, M.

18S rDNA sequence–structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida) Journal Article

In: Journal of Eukaryotic Microbiology, 2022.

Abstract | Links | BibTeX

Maciszewski, K.; Fells, A.; Karnkowska, A.

Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes Journal Article

In: Molecular biology and evolution, vol. 39, no. 12, pp. msac255, 2022.

Abstract | Links | BibTeX

Ebenezer, T. E.; Low, R. S.; O'Neill, E. C.; Huang, I.; DeSimone, A.; Farrow, S. C.; Field, R. A.; Ginger, M. L.; Guerrero, S. A.; Hammond, M.; Hampl, V.; Horst, G.; Ishikawa, T.; Karnkowska, A.; Linton, E. W.; Myler, P.; Nakazawa, M.; Cardol, P.; Sánchez-Thomas, R.; Saville, B. J.; Shah, M. R.; Simpson, A. G. B.; Sur, A.; Suzuki, K.; Tyler, K. M.; Zimba, P. V.; Hall, N.; Field, M. C.

Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world Journal Article

In: Biology open, vol. 11, no. 11, pp. bio059561, 2022.

Abstract | Links | BibTeX

Kaszecki, E.; Kennedy, V.; Shah, M.; Maciszewski, K.; Karnkowska, A.; Linton, E.; Ginger, M. L.; Farrow, S.; Ebenezer, T. E.

Meeting Report: Euglenids in the Age of Symbiogenesis: Origins, Innovations, and Prospects, November 8–11, 2021 Journal Article

In: Protist, vol. 173, no. 4, pp. 125894, 2022.

Links | BibTeX

Cho, A.; Tikhonenkov, D. V.; Hehenberger, E.; Karnkowska, A.; Mylnikov, A. P.; Keeling, P. J.

Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles Journal Article

In: Molecular Phylogenetics and Evolution, vol. 171, pp. 107468, 2022.

Abstract | Links | BibTeX

Karlicki, Michał; Antonowicz, Stanisław; Karnkowska, Anna

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

In: Bioinformatics, vol. 38, no. 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

In: Molecular Phylogenetics and Evolution, vol. 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

In: Microbial Genomics, vol. 7, no. 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

In: Open Biology, vol. 11, no. 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

In: Frontiers in Plant Science, vol. 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

In: Environmental Microbiology Reports, vol. 12, no. 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

In: Algal Research, vol. 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

In: Current Opinion in Genetics & Development, vol. 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

In: Journal of Phycology, vol. 55, no. 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

In: Molecular Biology and Evolution, vol. 36, no. 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

In: Scientific Reports, vol. 8, no. 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

In: Journal of Clinical Microbiology, vol. 56, no. 10, 2018, ISSN: 0095-1137.

Abstract | Links | BibTeX

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