publications

2024

  • Maciszewski, K., Wilga, G., Jagielski, T., Bakuła, Z., Gawor, J., Gromadka, R., & Karnkowska, A. (2024). Reduced plastid genomes of colorless facultative pathogens Prototheca (Chlorophyta) are retained for membrane transport genes. BMC Biology, 22(1), 294. https://doi.org/10.1186/s12915-024-02089-4
  • Karlicki, M., Bednarska, A., Hałakuc, P., Maciszewski, K., & Karnkowska, A. (2024). Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: Insights from metabarcoding and machine learning. FEMS Microbiology Ecology, 100(8). https://doi.org/10.1093/femsec/fiae104
  • Hollender, M., Sałek, M., Karlicki, M., & Karnkowska, A. (2024). Single-cell genomics revealed Candidatus Grellia alia sp. Nov. As an endosymbiont of Eutreptiella sp. (Euglenophyceae). Protist, 175(2).  https://doi.org/10.1016/j.protis.2024.126018
  • Kolisko, M., Maciszewski, K., & Karnkowska, A. (2024). Plastid Evolution in Non-photosynthetic Lineages. In Endosymbiotic Organelle Acquisition: Solutions to the Problem of Protein Localization and Membrane Passage (pp. 203–227). https://doi.org/10.1007/978-3-031-57446-7_7
  • Ginger, M. L., Karnkowska, A., Hampl, V., & Farrow, S. C. (2024). Basic biology, ecology, and biotechnology of euglenids. Protist, 175(6). https://doi.org/10.1016/j.protis.2024.126066
  • Qing, X., Karlicki, M., Guo, F., Karnkowska, A., & Li, H. (2024). Soil nematode community profiling using reference-free mito-metagenomics. Soil Biology and Biochemistry, 199. Scopus. https://doi.org/10.1016/j.soilbio.2024.109613
  • del Campo, J., Carlos-Oliveira, M., Čepička, I., Hehenberger, E., Horák, A., Karnkowska, A., Kolisko, M., Lara, E., Lukeš, J., Pánek, T., Piwosz, K., Richter, D. J., Škaloud, P., Sutak, R., Tachezy, J., & Hampl, V. (2024). The protist cultural renaissance. Trends in Microbiology, 32(2), 128–131. https://doi.org/10.1016/j.tim.2023.11.010

2023

  • Karnkowska, A., Yubuki, N., Maruyama, M., Yamaguchi, A., Kashiyama, Y., Suzaki, T., Keeling, P. J., Hampl, V., & Leander, B. S. (2022). Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis. PNAS, 120 (12) e2220100120. https://doi.org/10.1101/2022.11.29.517283
  • Hehenberger, E., Boscaro, V., James, E. R., Hirakawa, Y., Trznadel, M., Mtawali, M., Fiorito, R., del Campo, J., Karnkowska, A., Kolisko, M., Irwin, N. A. T., Mathur, V., Scheffrahn, R. H., & Keeling, P. J. (2023). 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 of Eukaryotic Microbiology, 70(5).  https://doi.org/10.1111/jeu.12987
  • Novák, L. V. F., Treitli, S. C., Pyrih, J., Hałakuc, P., Pipaliya, S. V., Vacek, V., Brzoň, O., Soukal, P., Eme, L., Dacks, J. B., Karnkowska, A., Eliáš, M., & Hampl, V. (2023). Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria. PLoS Genetics, 19(12).
  • Rackevei, A. S., Karnkowska, A., & Wolf, M. (2023). 18S rDNA sequence–structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida). Journal of Eukaryotic Microbiology, 70(2). https://doi.org/10.1111/jeu.12959
  • Žárský, V., Karnkowska, A., Boscaro, V., Trznadel, M., Whelan, T. A., Hiltunen-Thorén, M., Onut-Brännström, I., Abbott, C. L., Fast, N. M., Burki, F., & Keeling, P. J. (2023). Contrasting outcomes of genome reduction in mikrocytids and microsporidians. BMC Biology, 21(1). https://doi.org/10.1186/s12915-023-01635-w

2022

  • Karlicki, M., Antonowicz, S., & Karnkowska, A. (2022). Tiara: Deep learning-based classification system for eukaryotic sequences. Bioinformatics, 38(2), 344–350. https://doi.org/10.1093/bioinformatics/btab672
  • Cho, A., Tikhonenkov, D. V., Hehenberger, E., Karnkowska, A., Mylnikov, A. P., & Keeling, P. J. (2022). Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles. Molecular Phylogenetics and Evolution, 171. https://doi.org/10.1016/j.ympev.2022.107468
  • 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., … Field, M. C. (2022). Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world. Biology Open, 11(11). https://doi.org/10.1242/bio.059561
  • Hałakuc, P., Karnkowska, A., & Milanowski, R. (2022). Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans. BMC Ecology and Evolution, 22(1).  https://doi.org/10.1186/s12862-022-02014-9
  • Kaszecki, E., Kennedy, V., Shah, M., Maciszewski, K., Karnkowska, A., Linton, E., Ginger, M. L., Farrow, S., & Ebenezer, T. E. (2022). Meeting Report: Euglenids in the Age of Symbiogenesis: Origins, Innovations, and Prospects, November 8–11, 2021. 173(4). https://doi.org/10.1016/j.protis.2022.125894
  • Maciszewski, K., Dabbagh, N., Preisfeld, A., & Karnkowska, A. (2022). Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes. Molecular Phylogenetics and Evolution, 170. https://doi.org/10.1016/j.ympev.2022.107441
  • Maciszewski, K., Fells, A., & Karnkowska, A. (2022). Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes. Molecular Biology and Evolution, 39(12). Scopus. https://doi.org/10.1093/molbev/msac255

2021

  • Kostygov, A. Y., Karnkowska, A., Votýpka, J., Tashyreva, D., Maciszewski, K., Yurchenko, V., & Lukeš, J. (2021). Euglenozoa: Taxonomy, diversity and ecology, symbioses and viruses. Open Biology, 11(3). https://doi.org/10.1098/rsob.200407
  • Lax, G., Kolisko, M., Eglit, Y., Lee, W. J., Yubuki, N., Karnkowska, A., Leander, B. S., Burger, G., Keeling, P. J., & Simpson, A. G. B. (2021). Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Molecular Phylogenetics and Evolution, 159. https://doi.org/10.1016/j.ympev.2021.107088
  • Singh, R. A., Boscaro, V., James, E. R., Karnkowska, A., Kolisko, M., Gavelis, G. S., Okamoto, N., del Campo, J., Fiorito, R., Hehenberger, E., Irwin, N. A. T., Mathur, V., Scheffrahn, R. H., & Keeling, P. J. (2021). Characterization of new cristamonad species from kalotermitid termites including a novel genus, Runanympha. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-86645-w
  • Soukal, P., Hrdá, Š., Karnkowska, A., Milanowski, R., Szabová, J., Hradilová, M., Strnad, H., Vlček, Č., Čepička, I., & Hampl, V. (2021). Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Scientific Reports, 11(1), 13070. https://doi.org/10.1038/s41598-021-92174-3
  • Treitli, S. C., Pena-Diaz, P., Hałakuc, P., Karnkowska, A., & Hampl, V. (2021). High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis. Microbial Genomics, 7(12). https://doi.org/10.1099/MGEN.0.000745

2020

  • Bakuła, Z., Gromadka, R., Gawor, J., Siedlecki, P., Pomorski, J. J., Maciszewski, K., Gromadka, A., Karnkowska, A., & Jagielski, T. (2020). Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.01296
  • Kayama, M., Maciszewski, K., Yabuki, A., Miyashita, H., Karnkowska, A., & Kamikawa, R. (2020). Highly Reduced Plastid Genomes of the Non-photosynthetic Dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) Are Retained for tRNA-Glu-Based Organellar Heme Biosynthesis. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.602455
  • Keeling, P. J., Boscaro, V., Bardell, F., Burki, F., Cho, A., Cooney, E. C., del Campo, J., Fast, N. M., Fiorito, R., Gavelis, G. S., Gawryluk, R. M. R., George, E. E., Gomm-Kolisko, R. N., Grisdale, C. J., Heger, T., Hehenberger, E., Herranz, M., Hirakawa, Y., Husnik, F., … Wong, D. K. (2020). A letter to Denis Lynn. Aquatic Ecosystem Health and Management, 23(1), 17–18. https://doi.org/10.1080/14634988.2020.1717827
  • Kolisko, M., Flegontova, O., Karnkowska, A., Lax, G., Maritz, J. M., Pánek, T., Táborský, P., Carlton, J. M., Čepička, I., Horák, A., Lukeš, J., Simpson, A. G. B., & Tai, V. (2020). EukRef-excavates: Seven curated SSU ribosomal RNA gene databases. Database, 2020. https://doi.org/10.1093/database/baaa080
  • Lukešová, S., Karlicki, M., Tomečková Hadariová, L., Szabová, J., Karnkowska, A., & Hampl, V. (2020). Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. Environmental Microbiology Reports, 12(1), 78–91. https://doi.org/10.1111/1758-2229.12817

2019

  • Maciszewski, K., & Karnkowska, A. (2019). Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles. Current Opinion in Genetics and Development, 58–59, 33–39.  https://doi.org/10.1016/j.gde.2019.07.013
  • Adl, S. M., Bass, D., Lane, C. E., Lukeš, J., Schoch, C. L., Smirnov, A., Agatha, S., Berney, C., Brown, M. W., Burki, F., Cárdenas, P., Čepička, I., Chistyakova, L., del Campo, J., Dunthorn, M., Edvardsen, B., Eglit, Y., Guillou, L., Hampl, V., … Zhang, Q. (2019). Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology, 66(1), 4–119.
  • Han, K. Y., Maciszewski, K., Graf, L., Yang, J. H., Andersen, R. A., Karnkowska, A., & Yoon, H. S. (2019). Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization. Journal of Phycology, 55(5), 1166–1180.  https://doi.org/10.1111/jpy.12904
  • Jagielski, T., Bakuła, Z., Gawor, J., Maciszewski, K., Kusber, W.-H., Dyląg, M., Nowakowska, J., Gromadka, R., & Karnkowska, A. (2019). The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies. Algal Research, 43. Scopus. https://doi.org/10.1016/j.algal.2019.101639
  • Karnkowska, A., Treitli, S. C., Brzoň, O., Novák, L., Vacek, V., Soukal, P., Barlow, L. D., Herman, E. K., Pipaliya, S. V., Pánek, T., Žihala, D., Petrželková, R., Butenko, A., Eme, L., Stairs, C. W., Roger, A. J., Eliáš, M., Dacks, J. B., Hampl, V., & Battistuzzi, F. U. (2019). The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. Molecular Biology and Evolution, 36(10), 2292–2312. https://doi.org/10.1093/molbev/msz147

2018

  • Jagielski, T., Gawor, J., Bakuła, Z., Decewicz, P., Maciszewski, K., & Karnkowska, A. (2018). Cytb as a new genetic marker for differentiation of prototheca species. Journal of Clinical Microbiology, 56(10). https://doi.org/10.1128/JCM.00584-18
  • Karnkowska, A., Bennett, M. S., & Triemer, R. E. (2018). Dynamic evolution of inverted repeats in Euglenophyta plastid genomes. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-34457-w
  • Strassert, J. F. H., Karnkowska, A., Hehenberger, E., Del Campo, J., Kolisko, M., Okamoto, N., Burki, F., Janouškovec, J., Poirier, C., Leonard, G., Hallam, S. J., Richards, T. A., Worden, A. Z., Santoro, A. E., & Keeling, P. J. (2018). Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME Journal, 12(1), 304–308. https://doi.org/10.1038/ismej.2017.167