Personnel

Alexei Kostygov, Ph.D., postdoctoral researcher

Education: Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia. Ph.D. 2013

Publications

Kostygov, A.Y., Grybchuk-Ieremenko, A., Malysheva, M., Frolov, A., Yurchenko, V. Molecular revision of the genus Wallaceina. Protist, 2014, 165: 594-604. PMID: 25113831

Chistyakova, L., Kostygov, A.Y., Kornilova, O., Yurchenko, V. Reisolation and redescription of Balantidium duodeni Stein, 1867 (Litostomatea, Trichostomatia). Parasitol. Res., 2014, 113: 4207–4215. PMID: 25185665

Votýpka, J.*, Kostygov, A.Y.*, Kraeva, N., Grybchuk-Ieremenko, A., Tesařová, M., Grybchuk, D., Lukeš, J., Yurchenko, V. Kentomonas gen. n., a new genus of endosymbiont-containing trypanosomatids of Strigomonadinae subfam. n. Protist, 2014, 165: 825-838. * Equal contribution. PMID: 25460233

Grybchuk-Ieremenko, A., Losev, A., Kostygov, A.Y., Lukeš, J., Yurchenko, V. High prevalence of trypanosome co-infections in freshwater fishes. Folia Parasitol., 2014, 61: 495-504. PMID: 25651690

Losev, A., Grybchuk-Ieremenko, A., Kostygov, A.Y., Lukeš, J., Yurchenko, V. Host specificity, pathogenicity and mixed infections of trypanoplasms from freshwater fishes. Parasitol. Res., 2015, 114:1071–1078. PMID: 25544706

Kraeva, N., Butenko, A., Hlaváčová, J., Kostygov, A.Y., Myškova, J., Grybchuk, D., Leštinová, T., Votýpka, J., Volf, P., Opperdoes, F., Flegontov, P., Lukeš, J., Yurchenko, V. Leptomonas seymouri: adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co-infection with Leishmania donovani. PLoS Path., 2015, 11(8): e1005127. PMID: 226317207

d'Avila-Levy, C., Boucinha, C., Kostygov, A.Y., Santos, H. L. C., Morelli, K. A., Grybchuk-Ieremenko, A., Duval, L., Votýpka, J., Yurchenko, V., Grellier, P., Lukeš, J. Exploring environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era (Review). Mem Inst Oswaldo Cruz, 2015, 110(8): 956-965. PMID: 26602872

Frolov, A., Malysheva, M., Yurchenko, V., Kostygov, A.Y.* Back to monoxeny: Phytomonas nordicus descended from dixenous plant parasites. Eur. J. Protistol., 2016, 52 (1):1-10. * Correspondent author. PMID: 26555733

Yurchenko, V., Kostygov, A.Y., Havlová, J., Grybchuk-Ieremenko, A., Ševčíková, T., Lukeš, J., Ševčík, J., Votýpka, J. Diversity of trypanosomatids in cockroaches and the description of Herpetomonas tarakana sp. n. J. Euk. Microbiol., 2016, 63: 198-209. PMID: 26352484

Kostygov, A.Y.*, Dobáková, E.*, Grybchuk-Ieremenko, A.*, Váhala, D., Maslov, D., Votýpka, J., Lukeš, J., Yurchenko, V. Novel trypanosomatid – bacterium association: evolution of endosymbiosis in action. mBio, 2016, 7(2): e01985-15. * Equal contribution. PMID: 26980834

Flegontov, P., Butenko, A., Firsov. S., Kraeva, N., Eliáš, M., Field, M., Filatov, D., Flegontova, O., Gerasimov, E., Hlaváčová, J., Ishemgulova, A., Jackson, A., Kelly, S., Kostygov, A.Y., Logacheva, M., Maslov, D., Opperdoes, F., O'Reilly, A., Sádlová, J., Ševčíková, T., Venkatesh, D., Vlček, Č., Volf, P., Votýpka, J., Záhonová, K., Yurchenko, V., Lukeš, J. Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Sci. Rep., 2016, 6: 23704. PMID: 27021793

Záhonová, K.*, Kostygov, A.Y.*, Ševčíková, T., Yurchenko, V., Eliáš, M. An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons. Curr. Biol., 2016, 26: 2364-2369. * Equal contribution. PMID: 27593378

Kraeva, N., Horáková, E., Kostygov, A.Y., Kořený, L., Butenko, A., Yurchenko, V., Lukeš, J. Catalase in Leishmaniinae: with me or against me? Infect. Genet. Evol., 2017, 50: 121-127. PMID: 27381333

Frolov, A., Malysheva, M., Ganyukova, A., Yurchenko, V., Kostygov, A.Y.* Life cycle of Blastocrithidia papi sp. n. (Kinetoplastea, Trypanosomatidae) in Pyrrhocoris apterus (Hemiptera, Pyrrhocoridae). Eur. J. Protistol., 2017, 57: 85-98. * Correspondent author. PMID: 28073072

Ishemgulova, A., Butenko, A., Kortišová, L., Boucinha, C., Grybchuk-Ieremenko, A., Morelli, K.A., Tesařová, M., Kraeva, N., Grybchuk, D., Pánek, T., Flegontov, P., Lukeš, J., Votýpka, J., Galvão Pavan, M., Opperdoes, F.R., Spodareva, V., d'Avila-Levy, C., Kostygov, A.Y.*, Yurchenko, V.* Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila. PLoS One, 2017, 12(3): e0174165. * Co-correspondent authors. PMID: 28328988

Kostygov, A.Y., Yurchenko, V. Revised classification of the subfamily Leishmaniinae (Trypanosomatidae). Folia Parasitol., 2017, 64: 020. PMID: 28783029

Ishemgulova, A., Kraeva, N., Hlaváčová, J., Zimmer, S., Butenko, A., Podešvová, L., Leštinová, T., Lukeš, J., Kostygov, A.Y., Votýpka, J., Volf, P., Yurchenko, V. A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLoS Negl. Trop. Dis., 2017, 11(7): e0005782. PMID: 28742133

Kostygov, A.Y.*, Butenko, A.*, Nenarokova, A., Tashyreva, D., Flegontov, P., Lukeš, J., Yurchenko, V. Genome of Ca. Pandoraea novymonadis, an endosymbiotic bacterium of the trypanosomatid Novymonas esmeraldas. Front. Microbiol., 2017, 8: 1940. * Equal contribution. PMID: 29046673.

Butenko, A., da Silva Vieira, T., Frolov, A.O., Opperdoes, F.R., Soares, R.P., Kostygov, A.Y., Lukeš, J., Yurchenko, V. Leptomonas pyrrhocoris: genomic insight into parasite's physiology. Curr. Genomics, 2018, 19(2): 150-156. PMID: 29491743

Grybchuk, D., Akopyants. N.S., Kostygov, A.Y., Konovalovas, A., Lye, L.-F., Dobson, D.E., Zangger, H., Fasel. N., Butenko, A., Frolov. A.O., Votýpka, J., d'Avila-Levy, C.M., Kulich, P., Moravcová, J., Plevka, P., Rogozin, I.B., Serva, S., Lukeš, J., Beverley, S.M., Yurchenko, V. Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania. Proc. Natl. Acad. Sci. USA, 2018, 115(3): E506-E515. PMID: 29284754

Grybchuk, D., Kostygov, A.Y., Macedo, D.H., d'Avila-Levy, C.M., Yurchenko, V. RNA viruses in trypanosomatid parasites: a historical overview (Review). Mem. Inst. Oswaldo Cruz, 2018, 113(4): e170487. PMID: 29513877

Silva, F., Kostygov, A.Y., Spodareva, V., Butenko, A., Tossou, R., Lukeš, J., Yurchenko, V., Alves, J. The reduced genome of Candidatus Kinetoplastibacterium sorsogonicusi, the endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae): loss of the heme synthesis pathway. Parasitology, 2018, 145(10): 1287-1293. PMID: 29642956

Spodareva, V., Grybchuk-Ieremenko, A., Losev, A., Votýpka, J., Lukeš, J., Yurchenko, V.*, Kostygov, A.Y.* Diversity and evolution of anuran trypanosomes: insights from the study of European species. Parasit. Vectors, 2018, 11: 447. * Co-correspondent authors. PMID: 30071897

Frolov, A., Malysheva, M., Ganyukova, A., Yurchenko, V., Kostygov, A.Y.* Obligate development of Blastocrithidia papi (Trypanosomatidae) in the Malpighian tubules of Pyrrhocoris apterus (Hemiptera) and coordination of host-parasite life cycles. PLoS One, 2018, 13(9): e0204467. * Correspondent author. PMID: 30261003

Grybchuk, D., Kostygov, A.Y., Macedo, D.H., Votýpka, J., Lukeš, J., Yurchenko, V. RNA viruses in Blechomonas (Trypanosomatidae) and evolution of Leishmaniavirus. mBio, 2018, 9(5): e01932-18. PMID: 30327446

Maslov, D.A., Opperdoes, F.R., Kostygov, A.Y., Hashimi, H., Lukeš, J., Yurchenko, V. Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy, and evolution (Review). Parasitology, 2019, 146(1): 1-27. PMID: 29898792

Kostygov, A.Y., Butenko, A., Yurchenko, V. On monoxenous trypanosomatids from lesions of immunocompetent patients with suspected cutaneous leishmaniasis in Iran. Trop. Med. Int. Health, 2019, 24(1): 127-128. PMID: 30307678

Frolov, A.O, Malysheva, M.N., Ganyukova, A.I., Spodareva, V.V., Yurchenko, V., Kostygov, A.Y.* Development of Phytomonas lipae sp. n. (Kinetoplastea: Trypanosomatidae) in the true bug Coreus marginatus (Heteroptera: Coreidae) and insights into the evolution of life cycles in the genus Phytomonas. PLoS One, 2019, 14(4): e0214484. * Correspondent author. PMID: 30943229

Bianchi, C., Kostygov, A.Y., Kraeva, N., Záhonová, K., Horáková, E., Sobotka, R., Lukeš, J., Yurchenko, V. An enigmatic catalase of Blastocrithidia. Mol. Biohem. Parasitol., 2019, 232: 111199. PMID: 31276694

Butenko, A., Kostygov, A.Y., Sádlová, J., Kleschenko, Y., Bečvář, T., Podešvová, L., Macedo, D.H., Žihala, D., Lukeš, J., Bates, P.A., Volf, P., Opperdoes, F.R., Yurchenko, V. Comparative genomics of Leishmania (Mundinia). BMC Genomics, 2019, 20(1): 726. PMID: 31601168

Kraeva, N., Leštinová, T., Ishemgulova, A., Majerová, K., Butenko, A., Vaselek, S., Bespyatykh, J., Charyyeva, A., Spitzová, T., Kostygov, A.Y., Lukeš, J., Volf, P., Votýpka, J., Yurchenko, V. LmxM.22.0250-encoded dual specificity protein/lipid phosphatase impairs Leishmania mexicana virulence in vitro. Pathogens, 2019, 8: E241. PMID: 31744234

Králová, J., Grybchuk-Ieremenko, A., Votýpka, J., Novotný, V., Kment, P., Lukeš, J., Yurchenko, V.*, Kostygov, A.Y.* Insect trypanosomatids in Papua New Guinea: high endemism and diversity. Int. J. Parasitol., 2109, 49: 1075-1086. * Co-correspondent authors. PMID: 31734337

Frolov, A.O., Malysheva, M.N., Ganyukova, A.I., Spodareva, V.V., Králová, J., Yurchenko, V., Kostygov, A.Y.* If host is refractory, insistent parasite goes berserk: trypanosomatid Blastocrithidia raabei in the true bug Coreus marginatus. PLoS One, 2020, 15(1): e0227832. * Correspondent author. PMID: 31945116

Grybchuk, D., Macedo, D.H., Kleschenko, Y., Kraeva, N., Lukashev, A.N., Bates, P.A., Kulich, P., Leštinová, T., Volf, P., Kostygov, A.Y.*, Yurchenko, V.* The first non-LRV RNA virus in Leishmania. Viruses, 2020, 12: 168. * Co-correspondent authors. PMID: 32024293

Ganyukova, A.I., Frolov, A.O., Malysheva, M.N., Spodareva, V.V., Yurchenko, V., Kostygov, A.Y.* A novel endosymbiont-containing trypanosomatid Phytomonas borealis sp. n. from the predatory bug Picromerus bidens (Heteroptera, Pentatomidae). Folia Parasitol., 2020, 67: 004. * Correspondent author. PMID: 32350156

Kostygov, A.Y.*, Frolov, A.O., Malysheva, M.N., Ganyukova, A.I., Chistyakova, L.V., Tashyreva, D., Tesařová, M., Spodareva, V.V., Režnarová, J., Macedo, D., Butenko, A., d’Avila-Levy, C.M., Lukeš, J., Yurchenko, V. Vickermania gen. nov., trypanosomatids that use two joined flagella to resist midgut peristaltic flow within the fly host. BMC Biol., 2020, 18: 187. * Correspondent author. PMID: 33267865

Kostygov, A.Y., Karnkowska, A., Votýpka, J., Tashyreva, D., Maciszewski, K., Yurchenko, V., Lukeš, J. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Bio., 2021, 11: 200407. PMID: 33715388

Charyyeva, A., Çetinkaya, Ü., Özkan. B., Şahin, S., Yaprak, N., Şahin, I., Yurchenko, V.*, Kostygov, A.Y.* Genetic diversity of Leishmania tropica: unexpectedly complex distribution pattern. Acta Trop., 2021, 218: 105888. * Co-correspondent authors. PMID: 33713626

Albanaz, A.T.S.; Gerasimov, E.S.; Shaw, J.J.; Sádlová, J.; Lukeš, J.; Volf, P.; Opperdoes, F.R.; Kostygov, A.Y.; Butenko, A.; Yurchenko, V. Genome analysis of Endotrypanum and Porcisia spp., closest phylogenetic relatives of Leishmania, highlights the role of amastins in shaping pathogenicity. Genes. 2021, 12(3): 444. PMID: 33804709

Frolov, A.O.*, Kostygov,A.Y.*, Yurchenko, V.* Development of monoxenous trypanosomatids and phytomonads in insects. Trends Parasitol., 2021, 37(6): 538-551. * Co-correspondent authors. PMID: 33714646

Skalický, T., Alves, J.M.P., Morais, A.C., Režnarová, J., Butenko, A., Lukeš, J., Serrano, M.G., Buck, G.A., Teixeira, M.M.G., Camargo, E.P., Sanders, M., Cotton, J.A., Yurchenko, V., Kostygov,A.Y.* Endosymbiont capture, a repeated process of endosymbiont transfer with replacement in trypanosomatids Angomonas spp. Pathogens, 2021, 10: 702. * Correspondent author. PMID: 34200026

Kostygov,A.Y.*, Alves, J.M.P.*, Yurchenko, V.* Editorial: symbioses between protists and bacteria/archaea. Front. Microbiol., 2021, 12: 709184. * Co-correspondent authors. PMID: 34394058

Zakharova, A., Saura, A., Butenko, A., Podešvová, L., Warmusová, S., Kostygov,A.Y., Nenarokova, A., Lukeš, J., Opperdoes, F.R., Yurchenko, V. A new model trypanosomatid Novymonas esmeraldas: genomic perception of its "Candidatus Pandoraea novymonadis" endosymbiont. mBio, 2021, 12(4): e01606-21. PMID: 34399629

Yurchenko, V.*, Butenko, A., Kostygov, A.Y.* Genomics of Trypanosomatidae: where we stand and what needs to be done? Pathogens, 2021, 10: 1124. * Co-correspondent authors. PMID: 34578156

Kostygov, A.Y.*; Grybchuk, D., Kleschenko, Y., Chistyakov, D.S., Lukashev, A.N., Gerasimov, E.S., Yurchenko, V.* Analyses of Leishmania-LRV co-phylogenetic patterns and evolutionary variability of viral proteins. Viruses, 2021, 13(11): 2305. * Co-correspondent authors. PMID: 34835111

Chmelová, L’., Bianchi, C., Albanaz, A.T.S., Režnarová, J., Wheeler, R., Kostygov, A.Y., Kraeva, N., Yurchenko, V. Comparative analysis of three trypanosomatid catalases of different origin. Antioxidants, 2022, 11: 46. PMID: 35052550

Kostygov, A.Y.*, Frolov, A.O., Malysheva, M.N., Ganyukova, A.I., Drachko, D., Yurchenko, V., Agasoy, V.V. Development of two species of the Trypanosoma theileri complex in tabanids. Parasit. Vectors, 2022, 15: 95. * Correspondent author. PMID: 35313955

Saura, A., Zakharova, A., Klocek, D., Gerasimov, E.S., Butenko, A., Macedo, D.H., Servienė, E., Zagirova, D., Meshcheryakova, A., Rogozin, I.B., Serva, S., Kostygov, A.Y.*, Yurchenko, V.* Elimination of LRVs elicits different responses in Leishmania spp. mSphere, 2022, 7(4): e00335-22. * Co-correspondent authors. PMID: 35943162

Kostygov, A.Y.*, Malysheva, M.N., Ganyukova, A.I., Razygraev, A.V., Drachko, D.O., Yurchenko, V., Agasoi, V.V., Frolov, A.O. The roles of mosquitoes in the circulation of monoxenous trypanosomatids in temperate climates. Pathogens, 2022, 11: 1326. * Correspondent author. PMID: 36422578

Magri, A.*, Bianchi, C., Chmelová, L′., Caffara, M., Galuppi, R., Fioravanti, M., Yurchenko, V.*, Kostygov, A.Y.* Roe deer (Capreolus capreolus) are a novel potential reservoir for human visceral leishmaniasis in the Emilia-Romagna region of Northeastern Italy. Int. J. Parasitol., 2022, 52(12): 745-750. * Co-correspondent authors. PMID: 36265672

Jászayová, A., Režnarová, J., Chovancová, G., Kostygov, A.Y., Yurchenko, V., Antolová, D., Zwijacz-Kozica, T., Csanády, A., Hurníková, Z. A study of oribatid mites as potential intermediate hosts of anoplocephalid tapeworms of Tatra chamois and Tatra marmots from the Tatra Mountains, Central Europe, and report of a new intermediate host for Andrya cuniculi, the parasite of Leporidae. Life, 2023, 13(4): 955. PMID: 37109484

Zakharova, A., Tashyreva, D., Butenko, A., Morales, J., Saura, A., Svobodová, M., Poschmann, G., Nandipati, S., Zakharova, A., Noyvert, D., Gahura, O., Týč, J., Stühler, K., Kostygov, A.Y.*, Nowack, E.C.M., Lukeš, J., Yurchenko, V.* A neo-functionalized homolog of host transmembrane protein controls localization of bacterial endosymbionts in the trypanosomatid Novymonas esmeraldas. Curr. Biol., 2023, 33(13): 2690-2701. * Co-correspondent authors. PMID: 37201521

Albanaz, A.T.S., Butenko, A., Kostygov, A.Y., Votýpka, J., Yurchenko, V. Transcriptome of Lafontella sp., an obscure relative of Phytomonas and Herpetomonas. Protistology, 2023, 17(2): 109-117

Klocek, D., Grybchuk, D., Tichá, L., Votýpka, J., Volf, P., Kostygov, A.Y.*, Yurchenko, V.* Evolution of RNA viruses in trypanosomatids: new insights from the analysis of Sauroleishmania. Parasitol. Res., 2023, 122(10): 2279-2286. * Co-correspondent authors. PMID: 37490143

Albanaz, A.T.S., Carrington, M., Frolov, A.O., Ganyukova, A.I., Gerasimov, E.S., Kostygov, A.Y., Lukeš, J., Malysheva, M.N., Votýpka, J., Zakharova, A., Záhonová, K., Zimmer, S.L., Yurchenko, V., Butenko, A. Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae. BMC Genomics, 2023, 24: 471. PMID: 37605127

Macedo, D.H., Grybchuk, D., Režnarová, J., Votýpka, J., Klocek, D., Yurchenko, T., Ševčík, J., Magri, A., Urda Dolinská, M., Záhonová, K., Lukeš, J., Servienė, E., Jászayová, A., Serva, S., Malysheva, M.N., Frolov, A.O., Yurchenko, V.*, Kostygov, A.Y.* Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biol., 2023, 21(1): 191. * Co-correspondent authors. PMID: 37697369

Klocek, D., Grybchuk, D., Macedo, D.H., Galan, A., Votýpka, J., Schmid-Hempel, R., Schmid-Hempel, P., Yurchenko, V.*, Kostygov, A.Y.* RNA viruses of Crithidia bombi, a parasite of bumblebees. J. Invertebr. Pathol., 2023, 201: 107991. * Co-correspondent authors. PMID: 37714407

Kostygov, A.Y.*, Chmelová, L′., Reichl, J., Jászayová, A., Votýpka, J., Fuehrer, H.-P., Yurchenko, V.* Parasites of firebugs in Austria with focus on the "micro"-diversity of the cosmopolitan trypanosomatid Leptomonas pyrrhocoris. Parasitol. Res., 2024, 123(1): 27. * Co-correspondent authors. PMID: 38072883

Kostygov, A.Y.*#, Albanaz, A.T.S.#, Butenko, A., Gerasimov, E.S., Lukeš, J., Yurchenko, V.* Phylogenetic framework to explore trait evolution in Trypanosomatidae. Trends Parasitol., 2024, 40(2): 96-99. # shared contribution. * Co-correspondent authors. PMID: 38065790

Zavataro, A.L.E., Skýpalová, K., Vergara, P.O.T., Silva, F.M, Butenko, A., Yurchenko, V., Kostygov, A.Y., Alves, J.M.P. The genome of the endosymbiont-harboring trypanosomatid Kentomonas sorsogonicus. Protistology, 2024, 18(1): 72-81

Chmelová, L′., Kraeva, N., Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int. J. Parasitol., 2024, 54: 391-400. PMID: 38663543

Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol., 2024, 10(1): veae037. PMID: 38774311

Kostygov, A.Y.*, Skýpalová, K.*, Kraeva, N., Kalita, E., McLeod, C., Yurchenko, V., Field, M.C., Lukeš, J., Butenko, A. Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol., 22, 281. * Equal contribution. PMID: 39627879

Kostygov, A.Y., Grybchuk, D., Heeren, S., Gerasimov, E.S., Klocek, D., Reddy, A., Sádlová, J., Pacáková, L., Kohl, A., Stejskal, F., Volf, P., Dujardin, J.-C., Yurchenko, V. A novel strain of Leishmania braziliensis harbors not a toti- but a bunyavirus., PLoS Negl. Trop. Dis., 2024, 18(12): e0012767. PMID: 39729426

Grybchuk, D., Kostygov, A.Y., Yurchenko, V. Analysis of Leishbuviridae from trypanosomatids. In: Bunyaviruses: Methods and Protocols (Ed. H. Boshra), 2025, 2893: 151-167. ("Methods in Molecular Biology" Series v. 2893, Hardcover ISBN 978-1-0716-4337-2, Softcover ISBN 978-1-0716-4340-2, eBook ISBN 978-1-0716-4338-9, Series ISSN 1064-3745, Series E-ISSN 1940-6029). PMID: 39671036

Záhonová, K., Füssy, Z., Albanaz, A., Butenko, A., Kachale, A., Kraeva, N., Galan, A., Zakharova, A., Stojanova, B., Votýpka, J., Kostygov, A.Y., Spodareva, V., Malysheva, M.N., Frolov, A.O., Rogozin, I., Paris, Z., Valasek, L., Yurchenko, V., Lukeš, J. Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio, 2025, (accepted). PMID:

Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A.Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. Converting Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code, into a genetically-tractable model. Mol. Microbiol., 2025, (accepted). PMID:

Natalia Kraeva, Ph.D., postdoctoral researcher

Education: Ostravská Univerzita, Ostrava, Czech Republic. Ph.D. 2017

Publications

Votýpka, J., Suková, E., Kraeva, N., Ishemgulova, A., Duží, I., Lukeš, J., Yurchenko, V. Diversity of trypanosomatids (Kinetoplastea: Trypanosomatidae) parasitizing fleas (Insecta: Siphonaptera) and description of a new genus Blechomonas gen. n. Protist, 2013, 164: 763-781. PMID: 24113136

Yurchenko, V., Votýpka, J., Tesařová, M., Klepetková, H., Kraeva, N., Jirků, M., Lukeš, J. Ultrastructure and molecular phylogeny of four new species of monoxenous trypanosomatids from flies (Diptera: Brachycera) with redefinition of the genus Wallaceina. Folia Parasitol., 2014, 61: 97-112. PMID: 24822316

Votýpka, J., Kostygov, A., Kraeva, N., Grybchuk-Ieremenko, A., Tesařová, M., Grybchuk, D., Lukeš, J., Yurchenko, V. Kentomonas gen. n., a new genus of endosymbiont-containing trypanosomatids of Strigomonadinae subfam. n. Protist, 2014, 165: 825-838. PMID: 25460233

Kraeva, N., Ishemgulova, A., Lukeš, J., Yurchenko, V. Tetracycline-inducible gene expression system in Leishmania mexicana. Mol. Biochem. Parasitol., 2014, 198: 11-13. PMID: 25461484

Kraeva, N., Butenko, A., Hlaváčová, J., Kostygov, A., Myškova, J., Grybchuk, D., Leštinová, T., Votýpka, J., Volf, P., Opperdoes, F., Flegontov, P., Lukeš, J., Yurchenko, V. Leptomonas seymouri: adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co-infection with Leishmania donovani. PLoS Path., 2015, 11(8): e1005127. PMID: 226317207

Kozminsky, E., Kraeva, N., Ishemgulova, A., Dobáková, E., Lukeš, J., Kment, P., Yurchenko, V., Votýpka, J., Maslov, D. Host-specificity of monoxenous trypanosomatids: statistical analysis of the distribution and transmission patterns of the parasites from Neotropical Heteroptera. Protist, 2015, 166(5): 551-568. PMID: 26466163

Flegontov, P., Butenko, A., Firsov. S., Kraeva, N., Eliáš, M., Field, M., Filatov, D., Flegontova, O., Gerasimov, E., Hlaváčová, J., Ishemgulova, A., Jackson, A., Kelly, S., Kostygov. A., Logacheva, M., Maslov, D., Opperdoes, F., O'Reilly, A., Sádlová, J., Ševčíková, T., Venkatesh, D., Vlček, Č., Volf, P., Votýpka, J., Záhonová, K., Yurchenko, V., Lukeš, J. Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Sci. Rep., 2016, 6: 23704. PMID: 27021793

Ishemgulova, A., Kraeva, N., Faktorová, D., Podešvová, L., Lukeš, J., Yurchenko, V. T7 polymerase-driven transcription is downregulated in metacyclic promastigote and amastigote Leishmania mexicana. Folia Parasitol., 2016, 63: 016. PMID: 27311571

Kraeva, N.*, Horáková, E.*, Kostygov, A., Kořený, L., Butenko, A., Yurchenko, V., Lukeš, J. Catalase in Leishmaniinae: with me or against me? Infect. Genet. Evol., 2017, 50: 121-127. * Equal contribution. PMID: 27381333

Ishemgulova, A., Butenko, A., Kortišová, L., Boucinha, C., Grybchuk-Ieremenko, A., Morelli, K.A., Tesařová, M., Kraeva, N., Grybchuk, D., Pánek, T., Flegontov, P., Lukeš, J., Votýpka, J., Galvão Pavan, M., Opperdoes, F.R., Spodareva, V., d'Avila-Levy, C., Kostygov, A., Yurchenko, V. Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila. PLoS One, 2017, 12(3): e0174165. PMID: 28328988

Ishemgulova, A.*, Kraeva, N.*, Hlaváčová, J., Zimmer, S., Butenko, A., Podešvová, L., Leštinová, T., Lukeš, J., Kostygov, A., Votýpka, J., Volf, P., Yurchenko, V. A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLoS Negl. Trop. Dis., 2017, 11(7): e0005782. * Equal contribution. PMID: 28742133

Bianchi, C., Kostygov, A., Kraeva, N., Záhonová, K., Horáková, E., Sobotka, R., Lukeš, J., Yurchenko, V. An enigmatic catalase of Blastocrithidia. Mol. Biohem. Parasitol., 2019, 232: 111199. PMID: 31276694

Kraeva, N., Leštinová, T., Ishemgulova, A., Majerová, K., Butenko, A., Vaselek, S., Bespyatykh, J., Charyyeva, A., Spitzová, T., Kostygov, A.Y., Lukeš, J., Volf, P., Votýpka, J., Yurchenko, V. LmxM.22.0250-encoded dual specificity protein/lipid phosphatase impairs Leishmania mexicana virulence in vitro. Pathogens, 2019, 8: E241. PMID: 31744234

Grybchuk, D., Macedo, D.H., Kleschenko, Y., Kraeva, N., Lukashev, A.N., Bates, P.A., Kulich, P., Leštinová, T., Volf, P., Kostygov, A.Y., Yurchenko, V. The first non-LRV RNA virus in Leishmania. Viruses, 2020, 12: 168. PMID: 32024293

Gerasimov, E.S., Zamyatnina, K.A., Matveeva, N.S., Rudenskaya, Y.A., Kraeva, N., Kolesnikov, A.A., Yurchenko, V. Common structural patterns in the maxicircle divergent region of Trypanosomatidae. Pathogens, 2020, 9: 100. PMID: 32033466

Horáková, E., Faktorová, D., Kraeva, N., Kaur, B., Van Den Abbeele, J., Yurchenko, V., Lukeš, J. Catalase compromises the development of the insect and mammalian stages of Trypanosoma brucei. FEBS J., 2020, 287: 964-977. PMID: 31593329

Sádlová, J., Podešvová, L., Bečvář, T., Bianchi, C., Gerasimov, E.S., Saura, A., Glanzová, K., Leštinová, T., Matveeva, N.S., Chmelová, L., Mlacovská, D., Spitzová, T., Vojtková, B., Volf, P., Yurchenko, V.*, Kraeva, N.* Catalase impairs Leishmania mexicana development and virulence. Virulence, 2021, 12(1): 852-867. * Co-correspondent authors. PMID: 33724149

Gerasimov, E.S., Gasparyan, A.A., Afonin, D.A., Zimmer, S.L., Kraeva, N., Lukeš, J., Yurchenko, V., Kolesnikov, A. Complete minicircle genome of Leptomonas pyrrhocoris reveals a source of its non-canonical mitochondrial RNA editing events. Nucl. Acids Res., 2021, 49(6): 3354-3370. PMID: 33660779

Chmelová, L’., Bianchi, C., Albanaz, A.T.S., Režnarová, J., Wheeler, R., Kostygov, A.Y., Kraeva, N., Yurchenko, V. Comparative analysis of three trypanosomatid catalases of different origin. Antioxidants, 2022, 11: 46. PMID: 35052550

Chmelová, L′.*, Kraeva, N.*, Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int. J. Parasitol., 2024, 54: 391-400. * Equal contribution. PMID: 38663543

Kostygov, A.Y., Skýpalová, K., Kraeva, N., Kalita, E., McLeod, C., Yurchenko, V., Field, M.C., Lukeš, J., Butenko, A. Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol., 22, 281. PMID: 39627879

Záhonová, K., Füssy, Z., Albanaz, A., Butenko, A., Kachale, A., Kraeva, N., Galan, A., Zakharova, A., Stojanova, B., Votýpka, J., Kostygov, A.Y., Spodareva, V., Malysheva, M.N., Frolov, A.O., Rogozin, I., Paris, Z., Valasek, L., Yurchenko, V., Lukeš, J. Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio, 2025, (accepted). PMID:

Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A.Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. Converting Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code, into a genetically-tractable model. Mol. Microbiol., 2025, (accepted). PMID:

Andreu Saura, Ph.D., postdoctoral researcher

Education: Institute for Parasitology and Biomedicine “López-Neyra” (IPBLN-CSIC), National Spanish Research Council, Granada, Spain. Ph.D. 2018

Publications

Sádlová, J., Podešvová, L., Bečvář, T., Bianchi, C., Gerasimov, E.S., Saura, A., Glanzová, K., Leštinová, T., Matveeva, N.S., Chmelová, L., Mlacovská, D., Spitzová, T., Vojtková, B., Volf, P., Yurchenko, V., Kraeva, N. Catalase impairs Leishmania mexicana development and virulence. Virulence, 2021, 12(1): 852-867. PMID: 33724149

Rogozin, I.B., Roche-Lima, A., Tyryshkin, K., Carrasquillo-Carrión, K., Lada, A.G., Poliakov, L.Y., Schwartz, E., Saura, A., Yurchenko, V., Cooper, D.N., Panchenko, A.R., Pavlov, Y.I. DNA methylation, deamination and translesion synthesis combine to generate footprint mutations in cancer driver genes in B-cell derived lymphomas and other cancers. Front. Genetics, 2021, 12: 671866. PMID: 34093666

Zakharova, A., Saura, A., Butenko, A., Podešvová, L., Warmusová, S., Kostygov,A.Y., Nenarokova, A., Lukeš, J., Opperdoes, F.R., Yurchenko, V. A new model trypanosomatid Novymonas esmeraldas: genomic perception of its "Candidatus Pandoraea novymonadis" endosymbiont. mBio, 2021, 12(4): e01606-21. PMID: 34399629

Zakharova, A., Albanaz, A.T.S., Opperdoes, F.R., Škodová-Sveráková, I., Zagirova, D., Saura, A., Chmelová, L’., Gerasimov, E.S., Leštinová, T., Bečvář, T., Sádlová, J., Volf, P., Lukeš, J., Horváth, A., Butenko, A., Yurchenko, V. Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content. PLoS Negl. Trop. Dis., 2022, 16(6): e0010510. PMID: 35749562

Saura, A.*, Zakharova, A.*, Klocek, D., Gerasimov, E.S., Butenko, A., Macedo, D.H., Servienė, E., Zagirova, D., Meshcheryakova, A., Rogozin, I.B., Serva, S., Kostygov, A.Y., Yurchenko, V. Elimination of LRVs elicits different responses in Leishmania spp. mSphere, 2022, 7(4): e00335-22. * shared contrinution. PMID: 35943162

Rogozin, I.B., Saura, A., Bykova, A., Brover, V., Yurchenko, V. Deletions across the SARS-CoV-2 genome: molecular mechanisms and putative functional consequences of deletions in accessory genes. Microorganisms, 2023, 11: 229. PMID: 36677521

Zakharova, A., Tashyreva, D., Butenko, A., Morales, J., Saura, A., Svobodová, M., Poschmann, G., Nandipati, S., Zakharova, A., Noyvert, D., Gahura, O., Týč, J., Stühler, K., Kostygov, A.Y., Nowack, E.C.M., Lukeš, J., Yurchenko, V. A neo-functionalized homolog of host transmembrane protein controls localization of bacterial endosymbionts in the trypanosomatid Novymonas esmeraldas. Curr. Biol., 2023, 33(13): 2690-2701. PMID: 37201521

Bykova, A., Saura, A., Glazko, G.V., Roche-Lima, A., Yurchenko, V., Rogozin, I.B. The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection. BMC Genomics, 2023, 24(1): 387. PMID: 37430204

Usarov, G.X., Turitsin, V.S., Sattarova, X.G., Sádlová, J., ugli Mustanov, J.A., Saura, A., Yurchenko, V. Phlebotomine sand fly (Diptera: Phlebotominae) diversity in the foci of cutaneous leishmaniasis in the Surxondaryo Region of Uzbekistan: 50 years on. Parasitol. Res., 2024, 123: 170. PMID: 38526739

Rogozin, I.B., Saura, A., Poliakov, E., Bykova, A., Roche-Lima, A., Pavlov, Y.I., Yurchenko, V. Properties and mechanisms of deletions, insertions, and substitutions in the evolutionary history of SARS-CoV-2. Int. J. Mol. Sci., 2024, 25: 3696. PMID: 38612505

Chmelová, L′., Kraeva, N., Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int. J. Parasitol., 2024, 54: 391-400. PMID: 38663543

Gerasimov, E.S., Afonin, D.A., Škodová-Sveráková, I., Saura, A., Trusina, N., Gahura, O., Zakharova, A., Butenko, A., Baráth, P., Horváth, A., Opperdoes, F.R., Pérez-Morga, D., Zimmer, S.L., Lukeš, J., Yurchenko, V. Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatid Vickermania. Proc. Natl. Acad. Sci. USA, 2025, 122(15): e2426887122. PMID: 40203041

Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A.Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. Converting Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code, into a genetically-tractable model. Mol. Microbiol., 2025, (accepted). PMID:

Liudmyla Hrebenyk, Ph.D., postdoctoral researcher

Education: Kharkiv State University. Ph.D. 1996

Publications

Chmelová, L′., Záhonová, K., Albanaz, A.T.S., Hrebenyk, L., Horváth, A., Yurchenko, V., Škodová-Sveráková, I. Distribution and functional analysis of isocitrate dehydrogenases across kinetoplastids. Genome Biol. Evol., 2024, 16(3): evae042. PMID: 38447055

Edubiel Arturo Alpizar Sosa, DVM, Ph.D., postdoctoral researcher

Education: University og Glasgow. Ph.D. 2020

Rajendra Haribhau Mandage, Ph.D., postdoctoral researcher

Education: University of Pompeu Fabra. Ph.D. 2018

Publications

Záhonová, K., Mandage, R., Yurchenko, V. Nuclear genome assembly and annotation of kinetoplastids. In: Euglenozoa: Methods and Protocols (Eds. P. Michels, M. Ginger, L.-I. McCall, A. Silber, A. Karnkowska), 2025, (accepted). PMID:

Anzhelika Butenko, Ph.D., postdoctoral researcher (part-time)

Education: Ostravská Univerzita, Ostrava, Czech Republic. Ph.D. 2017

Publications

Kraeva, N., Butenko, A., Hlaváčová, J., Kostygov, A.Y., Myškova, J., Grybchuk, D., Leštinová, T., Votýpka, J., Volf, P., Opperdoes, F., Flegontov, P., Lukeš, J., Yurchenko, V. Leptomonas seymouri: adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co-infection with Leishmania donovani. PLoS Path., 2015, 11(8): e1005127. PMID: 226317207

Flegontov, P.*, Butenko, A.*, Firsov. S., Kraeva, N., Eliáš, M., Field, M., Filatov, D., Flegontova, O., Gerasimov, E., Hlaváčová, J., Ishemgulova, A., Jackson, A., Kelly, S., Kostygov. A.Y., Logacheva, M., Maslov, D., Opperdoes, F., O'Reilly, A., Sádlová, J., Ševčíková, T., Venkatesh, D., Vlček, Č., Volf, P., Votýpka, J., Záhonová, K., Yurchenko, V., Lukeš, J. Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Sci. Rep., 2016, 6: 23704. * Equal contribution. PMID: 27021793

Opperdoes, F.*, Butenko, A.*, Flegontov, P., Yurchenko, V., Lukeš, J. Comparative metabolism of free-living Bodo saltans and parasitic trypanosomatids. J. Euk. Microbiol., 2016, 63(5): 657-678. * Equal contribution. PMID: 27009761

Kraeva, N., Horáková, E., Kostygov, A.Y., Kořený, L., Butenko, A., Yurchenko, V., Lukeš, J. Catalase in Leishmaniinae: with me or against me? Infect. Genet. Evol., 2017, 50: 121-127. PMID: 27381333

Ishemgulova, A., Butenko, A., Kortišová, L., Boucinha, C., Grybchuk-Ieremenko, A., Morelli, K.A., Tesařová, M., Kraeva, N., Grybchuk, D., Pánek, T., Flegontov, P., Lukeš, J., Votýpka, J., Galvão Pavan, M., Opperdoes, F.R., Spodareva, V., d'Avila-Levy, C., Kostygov, A.Y., Yurchenko, V. Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila. PLoS One, 2017, 12(3): e0174165. PMID: 28328988

Ishemgulova, A., Kraeva, N., Hlaváčová, J., Zimmer, S., Butenko, A., Podešvová, L., Leštinová, T., Lukeš, J., Kostygov, A.Y., Votýpka, J., Volf, P., Yurchenko, V.* A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLoS Negl. Trop. Dis., 2017, 11(7): e0005782. PMID: 28742133

Lukša, J., Ravoitytė, B., Konovalovas, A., Aitmanaitė, L., Butenko, A., Yurchenko, V., Serva, S., Servienė, E. Different metabolic pathways are involved in response of Saccharomyces cerevisiae to L-A and M viruses. Toxins, 2017, 9: e233. PMID: 28757599

Kostygov, A.Y., Butenko, A., Nenarokova, A., Tashyreva, D., Flegontov, P., Lukeš, J., Yurchenko, V. Genome of Ca. Pandoraea novymonadis, an endosymbiotic bacterium of the trypanosomatid Novymonas esmeraldas. Front. Microbiol., 2017, 8: 1940. PMID: 29046673

Grybchuk, D., Akopyants. N.S., Kostygov, A.Y., Konovalovas, A., Lye, L.-F., Dobson, D.E., Zangger, H., Fasel. N., Butenko, A., Frolov. A.O., Votýpka, J., d'Avila-Levy, C.M., Kulich, P., Moravcová, J., Plevka, P., Rogozin, I.B., Serva, S., Lukeš, J., Beverley, S.M., Yurchenko, V. Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania. Proc. Natl. Acad. Sci. USA, 2018, 115(3): E506-E515. PMID: 29284754

Ishemgulova, A., Hlaváčová, J., Majerová, K., Butenko, A., Lukeš, J., Votýpka, J., Volf, P., Yurchenko, V. CRISPR/Cas9 in Leishmania mexicana: a case study of LmxBTN1. PLoS One, 2018, 13(2): e0192723. PMID: 29438445

Butenko, A., da Silva Vieira, T., Frolov, A.O., Opperdoes, F.R., Soares, R.P., Kostygov, A.Y., Lukeš, J., Yurchenko, V. Leptomonas pyrrhocoris: genomic insight into parasite's physiology. Curr. Genomics, 2018, 19(2): 150-156. PMID: 29491743

Záhonová, K., Petrželková, R., Valach, M., Yazaki, E., Tikhonenkov, D., Butenko, A., Janouškovec, J., Hrdá, Š., Klimeš, V., Burger, G., Inagaki, Y., Keeling, P., Hampl, V., Flegontov, P., Yurchenko, V., Eliáš, M. Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. Sci. Rep., 2018, 8: 5239. PMID: 29588502

Lukeš, J., Butenko, A., Hashimi, H., Maslov, D.A., Votýpka, J., Yurchenko, V. Trypanosomatids are much more than just trypanosomes: clues from the expanded family tree. Trends Parasitol., 2018, 34 (6): 466-480. PMID: 29605546

Silva, F., Kostygov, A.Y., Spodareva, V., Butenko, A., Tossou, R., Lukeš, J., Yurchenko, V., Alves, J. The reduced genome of Candidatus Kinetoplastibacterium sorsogonicusi, the endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae): loss of the heme synthesis pathway. Parasitology, 2018, 145(10): 1287-1293. PMID: 29642956

Kostygov, A.Y., Butenko, A., Yurchenko, V. On monoxenous trypanosomatids from lesions of immunocompetent patients with suspected cutaneous leishmaniasis in Iran. Trop. Med. Int. Health, 2019, 24(1): 127-128. PMID: 30307678

Butenko, A., Kostygov, A.Y., Sádlová, J., Kleschenko, Y., Bečvář, T., Podešvová, L., Macedo, D.H., Žihala, D., Lukeš, J., Bates, P.A., Volf, P., Opperdoes, F.R., Yurchenko, V. Comparative genomics of Leishmania (Mundinia). BMC Genomics, 2019, 20(1): 726. PMID: 31601168

Kraeva, N., Leštinová, T., Ishemgulova, A., Majerová, K., Butenko, A., Vaselek, S., Bespyatykh, J., Charyyeva, A., Spitzová, T., Kostygov, A.Y., Lukeš, J., Volf, P., Votýpka, J., Yurchenko, V. LmxM.22.0250-encoded dual specificity protein/lipid phosphatase impairs Leishmania mexicana virulence in vitro. Pathogens, 2019, 8: E241. PMID: 31744234

d’Avila-Levy, C.M., Bearzatto, B., Ambroise, J., Helaers, R., Butenko, A., Yurchenko, V., Morelli, K.A., Santos, H.L.C., Brouillard, P., Grellier, P., Gala, J.-L., Vikkula, M. First draft genome of the trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore technology and Illumina sequencing. Trop. Med. Infect. Dis., 2020, 5: 25. PMID: 32069939

Kostygov, A.Y., Frolov, A.O., Malysheva, M.N., Ganyukova, A.I., Chistyakova, L.V., Tashyreva, D., Tesařová, M., Spodareva, V.V., Režnarová, J., Macedo, D., Butenko, A., d’Avila-Levy, C.M., Lukeš, J., Yurchenko, V. Vickermania gen. nov., trypanosomatids that use two joined flagella to resist midgut peristaltic flow within the fly host. BMC Biol., 2020, 18: 187. PMID: 33267865

Durante, I.*, Butenko, A.*, Rašková, V., Charyyeva, A., Svobodová, M., Yurchenko, V., Hashimi, H., Lukeš, J. Large-scale phylogenetic analysis of trypanosomatid adenylate cyclases reveals associations with extracellular lifestyle and host-pathogen interplay. Genome Biol. Evol., 2020, 12(12): 2403-2416. * Equal contribution. PMID: 33104188

Opperdoes, F.R., Butenko, A., Zakharova, A., Gerasimov, E.S., Zimmer, S.L., Lukeš, J., Yurchenko, V. The remarkable metabolism of Vickermania ingenoplastis: genomic predictions. Pathogens, 2021, 10: 68. PMID: 33466586

Butenko, A., Hammond, M., Field, M., Ginger, M., Yurchenko, V., Lukeš, J. Reductionist pathways for parasitism in euglenozoans? Expanded datasets provide new insights. Trends Parasitol., 2021, 37(2): 100-116. (Review). PMID: 33127331

Albanaz, A.T.S., Gerasimov, E.S., Shaw, J.J., Sádlová, J., Lukeš, J., Volf, P., Opperdoes, F.R., Kostygov, A.Y., Butenko, A.*, Yurchenko, V.* Genome analysis of Endotrypanum and Porcisia spp., closest phylogenetic relatives of Leishmania, highlights the role of amastins in shaping pathogenicity. Genes. 2021, 12(3): 444. * Co-correspondent authors. PMID: 33804709

Poláková, E., Záhonová, K., Albanaz, A.T.S., Butenko, A., Lukeš, J., Yurchenko, V. Diverse telomeres in trypanosomatids. Parasitology, 2021, 148: 1254-1270. PMID: 33612129

Skalický, T., Alves, J.M.P., Morais, A.C., Režnarová, J., Butenko, A., Lukeš, J., Serrano, M.G., Buck, G.A., Teixeira, M.M.G., Camargo, E.P., Sanders, M., Cotton, J.A., Yurchenko, V., Kostygov,A.Y. Endosymbiont capture, a repeated process of endosymbiont transfer with replacement in trypanosomatids Angomonas spp. Pathogens, 2021, 10: 702. PMID: 34200026

Zakharova, A., Saura, A., Butenko, A., Podešvová, L., Warmusová, S., Kostygov, A.Y., Nenarokova, A., Lukeš, J., Opperdoes, F.R., Yurchenko, V. A new model trypanosomatid Novymonas esmeraldas: genomic perception of its "Candidatus Pandoraea novymonadis" endosymbiont. mBio, 2021, 12(4): e01606-21. PMID: 34399629

Yurchenko, V., Butenko, A., Kostygov, A.Y. Genomics of Trypanosomatidae: where we stand and what needs to be done? Pathogens, 2021, 10: 1124. PMID: 34578156

Zakharova, A., Albanaz, A.T.S., Opperdoes, F.R., Škodová-Sveráková, I., Zagirova, D., Saura, A., Chmelová, L’., Gerasimov, E.S., Leštinová, T., Bečvář, T., Sádlová, J., Volf, P., Lukeš, J., Horváth, A., Butenko, A., Yurchenko, V. Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content. PLoS Negl. Trop. Dis., 2022, 16(6): e0010510. PMID: 35749562

Saura, A., Zakharova, A., Klocek, D., Gerasimov, E.S., Butenko, A., Macedo, D.H., Servienė, E., Zagirova, D., Meshcheryakova, A., Rogozin, I.B., Serva, S., Kostygov, A.Y., Yurchenko, V. Elimination of LRVs elicits different responses in Leishmania spp. mSphere, 2022, 7(4): e00335-22. PMID: 35943162

Zakharova, A., Tashyreva, D., Butenko, A., Morales, J., Saura, A., Svobodová, M., Poschmann, G., Nandipati, S., Zakharova, A., Noyvert, D., Gahura, O., Týč, J., Stühler, K., Kostygov, A.Y., Nowack, E.C.M., Lukeš, J., Yurchenko, V. A neo-functionalized homolog of host transmembrane protein controls localization of bacterial endosymbionts in the trypanosomatid Novymonas esmeraldas. Curr. Biol., 2023, 33(13): 2690-2701. PMID: 37201521

Albanaz, A.T.S., Butenko, A.*, Kostygov, A.Y., Votýpka, J., Yurchenko, V. Transcriptome of Lafontella sp., an obscure relative of Phytomonas and Herpetomonas. Protistology, 2023, 17(2): 109-117. * Correspondent author.

Albanaz, A.T.S., Carrington, M., Frolov, A.O., Ganyukova, A.I., Gerasimov, E.S., Kostygov, A.Y., Lukeš, J., Malysheva, M.N., Votýpka, J., Zakharova, A., Záhonová, K., Zimmer, S.L., Yurchenko, V.*, Butenko, A.* Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae. BMC Genomics, 2023, 24: 471. * Co-correspondent authors. PMID: 37605127

Kostygov, A.Y., Albanaz, A.T.S., Butenko, A., Gerasimov, E.S., Lukeš, J., Yurchenko, V. Phylogenetic framework to explore trait evolution in Trypanosomatidae. Trends Parasitol., 2024, 40(2): 96-99. PMID: 38065790

Zavataro, A.L.E., Skýpalová, K., Vergara, P.O.T., Silva, F.M, Butenko, A., Yurchenko, V., Kostygov, A.Y., Alves, J.M.P. The genome of the endosymbiont-harboring trypanosomatid Kentomonas sorsogonicus. Protistology, 2024, 18(1): 72-81

Chmelová, L′., Kraeva, N., Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int. J. Parasitol., 2024, 54: 391-400. PMID: 38663543

Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol., 2024, 10(1): veae037. PMID: 38774311

Kostygov, A.Y., Skýpalová, K., Kraeva, N., Kalita, E., McLeod, C., Yurchenko, V., Field, M.C., Lukeš, J., Butenko, A.* Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol., 22, 281. * Correspondent author. PMID: 39627879

Gerasimov, E.S., Afonin, D.A., Škodová-Sveráková, I., Saura, A., Trusina, N., Gahura, O., Zakharova, A., Butenko, A., Baráth, P., Horváth, A., Opperdoes, F.R., Pérez-Morga, D., Zimmer, S.L., Lukeš, J., Yurchenko, V. Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatid Vickermania. Proc. Natl. Acad. Sci. USA, 2025, 122(15): e2426887122. PMID: 40203041

Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A.Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. Converting Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code, into a genetically-tractable model. Mol. Microbiol., 2025, (accepted). PMID:

Záhonová, K., Füssy, Z., Albanaz, A., Butenko, A., Kachale, A., Kraeva, N., Galan, A., Zakharova, A., Stojanova, B., Votýpka, J., Kostygov, A.Y., Spodareva, V., Malysheva, M.N., Frolov, A.O., Rogozin, I., Paris, Z., Valasek, L., Yurchenko, V., Lukeš, J. Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio, 2025, (accepted). PMID:

Kristína Pašuthová (Záhonová), Ph.D., postdoctoral researcher (part-time)

Education: Ostravská Univerzita, Ostrava, Czech Republic. Ph.D. 2016

Publications

Záhonová, K., Hadariová, L., Vacula, R., Yurchenko, V., Eliáš, M., Krajčovič, J., Vesteg, M. A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis. FEBS Lett., 2014, 588: 783-788. PMID: 24492004

Flegontov, P., Butenko, A., Firsov. S., Kraeva, N., Eliáš, M., Field, M., Filatov, D., Flegontova, O., Gerasimov, E., Hlaváčová, J., Ishemgulova, A., Jackson, A., Kelly, S., Kostygov. A.Y., Logacheva, M., Maslov, D., Opperdoes, F., O'Reilly, A., Sádlová, J., Ševčíková, T., Venkatesh, D., Vlček, Č., Volf, P., Votýpka, J., Záhonová, K., Yurchenko, V., Lukeš, J. Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Sci. Rep., 2016, 6: 23704. PMID: 27021793

Záhonová, K., Füssy, Z., Oborník, M., Eliáš, M., Yurchenko, V. RuBisCO in non-photosynthetic alga Euglena longa: divergent features, transcriptomic analysis and regulation of complex formation. PLoS One, 2016, 11(7): e0158790. PMID: 27391690

Záhonová, K.*, Kostygov, A.Y.*, Ševčíková, T., Yurchenko, V., Eliáš, M. An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons. Curr. Biol., 2016, 26: 2364-2369. * Equal contribution. PMID: 27593378

Záhonová, K., Petrželková, R., Valach, M., Yazaki, E., Tikhonenkov, D., Butenko, A., Janouškovec, J., Hrdá, Š., Klimeš, V., Burger, G., Inagaki, Y., Keeling, P., Hampl, V., Flegontov, P., Yurchenko, V., Eliáš, M. Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. Sci. Rep., 2018, 8: 5239. PMID: 29588502

Nenarokova, A., Záhonová, K., Krasilnikova, M., Gahura, O., McCulloch, R., Zíková, A., Yurchenko, V., Lukeš, J. Causes and effects of loss of classical non-homologous end joining pathway in parasitic eukaryotes. mBio, 2019, 10(4): e01541-19. PMID: 31311886

Bianchi, C., Kostygov, A.Y., Kraeva, N., Záhonová, K., Horáková, E., Sobotka, R., Lukeš, J., Yurchenko, V. An enigmatic catalase of Blastocrithidia. Mol. Biohem. Parasitol., 2019, 232: 111199. PMID: 31276694

Škodová-Sveráková, I.*, Záhonová, K.*, Bučková, B., Füssy, Z., Yurchenko, V., Lukeš, J. Catalase and ascorbate peroxidase in euglenozoan protists. Pathogens, 2020, 9: 317.* Equal contribution. PMID: 32344595

Füssy, Z.*, Záhonová, K.*, Tomčala, A., Krajčovič, J., Yurchenko, V., Oborník, M., Eliáš, M. The cryptic plastid of Euglena longa defines a new type of nonphotosynthetic plastid organelles. mSphere, 2020, 5(5): e00675-20. * Equal contribution. PMID: 33087518

Poláková, E., Záhonová, K., Albanaz, A.T.S., Butenko, A., Lukeš, J., Yurchenko, V. Diverse telomeres in trypanosomatids. Parasitology, 2021, 148: 1254-1270. PMID: 33612129

Kachale, A., Pavlíková, Z., Nenarokova, A., Roithová, A., Durante, I.M., Miletínová, P., Záhonová, K., Nenarokov, S., Votýpka, J., Horáková, E., Ross, R.L., Yurchenko, V., Beznosková, P., Paris, Z., Valášek, L.S., Lukeš, J. Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment. Nature, 2023, 613(7945): 751-758. PMID: 36631608

Albanaz, A.T.S., Carrington, M., Frolov, A.O., Ganyukova, A.I., Gerasimov, E.S., Kostygov, A.Y., Lukeš, J., Malysheva, M.N., Votýpka, J., Zakharova, A., Záhonová, K., Zimmer, S.L., Yurchenko, V., Butenko, A. Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae. BMC Genomics, 2023, 24: 471. PMID: 37605127

Macedo, D.H., Grybchuk, D., Režnarová, J., Votýpka, J., Klocek, D., Yurchenko, T., Ševčík, J., Magri, A., Urda Dolinská, M., Záhonová, K., Lukeš, J., Servienė, E., Jászayová, A., Serva, S., Malysheva, M.N., Frolov, A.O., Yurchenko, V., Kostygov, A.Y. Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biol., 2023, 21(1): 191. PMID: 37697369

Opperdoes, F.R.*, Záhonová, K.*, Škodová-Sveráková, I.*, Bučková, B., Chmelová, L′., Lukeš, J., Yurchenko, V. In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics, 2024, 25(1): 184. * Equal contribution. PMID: 38365628

Chmelová, L′., Záhonová, K., Albanaz, A.T.S., Hrebenyk, L., Horváth, A., Yurchenko, V., Škodová-Sveráková, I. Distribution and functional analysis of isocitrate dehydrogenases across kinetoplastids. Genome Biol. Evol., 2024, 16(3): evae042. PMID: 38447055

Afonin, D.A., Gerasimov, E.S., Škodová-Sveráková, I., Záhonová, K., Gahura, O., Albanaz, A.T.S., Myšková, E., Bykova, A., Paris, Z., Lukeš, J., Opperdoes, F.R., Horváth, A., Zimmer, S.L., Yurchenko, V. Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucl. Acids Res., 2024, 52: 3870–3885. PMID: 38452217

Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol., 2024, 10(1): veae037. PMID: 38774311

Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A.Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. Converting Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code, into a genetically-tractable model. Mol. Microbiol., 2025, (accepted). PMID:

Záhonová, K., Füssy, Z., Albanaz, A., Butenko, A., Kachale, A., Kraeva, N., Galan, A., Zakharova, A., Stojanova, B., Votýpka, J., Kostygov, A.Y., Spodareva, V., Malysheva, M.N., Frolov, A.O., Rogozin, I., Paris, Z., Valasek, L., Yurchenko, V., Lukeš, J. Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio, 2025, (accepted). PMID:

Záhonová, K., Mandage, R., Yurchenko, V. Nuclear genome assembly and annotation of kinetoplastids. In: Euglenozoa: Methods and Protocols (Eds. P. Michels, M. Ginger, L.-I. McCall, A. Silber, A. Karnkowska), 2025, (accepted). PMID:

Danil Grybchuk, Ph.D., postdoctoral researcher (part-time)

Education: Ostravská Univerzita, Ostrava, Czech Republic. Ph.D. 2017

Publications

Votýpka, J., Kostygov, A.Y., Kraeva, N., Grybchuk-Ieremenko, A., Tesařová, M., Grybchuk, D., Lukeš, J., Yurchenko, V. Kentomonas gen. n., a new genus of endosymbiont-containing trypanosomatids of Strigomonadinae subfam. n. Protist, 2014, 165: 825-838. PMID: 25460233

Kraeva, N., Butenko, A., Hlaváčová, J., Kostygov, A.Y., Myškova, J., Grybchuk, D., Leštinová, T., Votýpka, J., Volf, P., Opperdoes, F., Flegontov, P., Lukeš, J., Yurchenko, V. Leptomonas seymouri: adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co-infection with Leishmania donovani. PLoS Path., 2015, 11(8): e1005127. PMID: 226317207

Ishemgulova, A., Butenko, A., Kortišová, L., Boucinha, C., Grybchuk-Ieremenko, A., Morelli, K.A., Tesařová, M., Kraeva, N., Grybchuk, D., Pánek, T., Flegontov, P., Lukeš, J., Votýpka, J., Galvão Pavan, M., Opperdoes, F.R., Spodareva, V., d'Avila-Levy, C., Kostygov, A.Y., Yurchenko, V. Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila. PLoS One, 2017, 12(3): e0174165. PMID: 28328988

Grybchuk, D., Akopyants. N.S., Kostygov, A.Y., Konovalovas, A., Lye, L.-F., Dobson, D.E., Zangger, H., Fasel. N., Butenko, A., Frolov. A.O., Votýpka, J., d'Avila-Levy, C.M., Kulich, P., Moravcová, J., Plevka, P., Rogozin, I.B., Serva, S., Lukeš, J., Beverley, S.M., Yurchenko, V. Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania. Proc. Natl. Acad. Sci. USA, 2018, 115(3): E506-E515. PMID: 29284754

Grybchuk, D., Kostygov, A.Y., Macedo, D.H., d'Avila-Levy, C.M., Yurchenko, V. RNA viruses in trypanosomatid parasites: a historical overview (Review). Mem. Inst. Oswaldo Cruz, 2018, 113(4): e170487. PMID: 29513877

Grybchuk, D., Kostygov, A.Y., Macedo, D.H., Votýpka, J., Lukeš, J., Yurchenko, V. RNA viruses in Blechomonas (Trypanosomatidae) and evolution of Leishmaniavirus. mBio, 2018, 9(5): e01932-18. PMID: 30327446

Kleschenko, Y.*, Grybchuk, D.*, Matveeva, N.S., Macedo, D.H., Ponirovsky, E.N., Lukashev, A.N., Yurchenko, V. Molecular characterization of LRV2 in Leishmania major from Uzbekistan. Genes, 2019, 10: E830. * Equal contribution. PMID: 31640177

Grybchuk, D.*, Macedo, D.H.*, Kleschenko, Y., Kraeva, N., Lukashev, A.N., Bates, P.A., Kulich, P., Leštinová, T., Volf, P., Kostygov, A.Y., Yurchenko, V. The first non-LRV RNA virus in Leishmania. Viruses, 2020, 12: 168. * Equal contribution. PMID: 32024293

Procházková, M., Füzik, T., Grybchuk, D., Falginella, F., Podešvová, L., Yurchenko, V., Vácha, R., Plevka, P. Capsid structure of Leishmania RNA virus 1. J. Virol., 2021, 95(3): e01957-20. PMID: 33208443

Kostygov, A.Y.*; Grybchuk, D.*, Kleschenko, Y., Chistyakov, D.S., Lukashev, A.N., Gerasimov, E.S., Yurchenko, V. Analyses of Leishmania-LRV co-phylogenetic patterns and evolutionary variability of viral proteins. Viruses, 2021, 13(11): 2305. * Equal contribution. PMID: 34835111

Grybchuk, D., Procházková, M., Füzik, T., Konovalovas, A., Serva, S., Yurchenko, V., Plevka, P. Structures of L-BC virus and its open particle provide insight into Totivirus capsid assembly. Commun. Biol., 2022, 5(1): 847. PMID: 35986212

Procházková, M., Füzik, T., Grybchuk, D., Yurchenko, V., Plevka, P. Virion structure of Leishmania RNA virus 1. Virology, 2022, 577: 149-154. PMID: 36371873

Klocek, D., Grybchuk, D., Tichá, L., Votýpka, J., Volf, P., Kostygov, A.Y., Yurchenko, V. Evolution of RNA viruses in trypanosomatids: new insights from the analysis of Sauroleishmania. Parasitol. Res., 2023, 122(10): 2279-2286. PMID: 37490143

Rêgo, F.D., da Silva, E.S., Lopes, V.V., Teixeira-Neto, R.G., Belo, V.S., Fonseca Júnior, A.A., Pereira, D.A., Pena, H.P., Laurenti, M.D., Flores, G.V.A., da Matta, V.L.R., Chouman, I.H., Burrin, T.B., Pacheco, C.M.S., Barrouin-Melo, S.M., de Pinho, F.A., de Andrade, H.A., Nunes, R.V., Gontijo, C.M.F., Soccol, V.T., Klocek, D., Grybchuk, D., Macedo, D.H., do Monte-Neto, R.L., Yurchenko, V., Soares, R.P. First report of putative Leishmania RNA virus 2 (LRV2) in Leishmania infantum strains from canine and human visceral leishmaniasis cases in the Southeast of Brazil. Mem. Inst. Oswaldo Cruz, 2023, 118: e230071. PMID: 37729273

Macedo, D.H., Grybchuk, D., Režnarová, J., Votýpka, J., Klocek, D., Yurchenko, T., Ševčík, J., Magri, A., Urda Dolinská, M., Záhonová, K., Lukeš, J., Servienė, E., Jászayová, A., Serva, S., Malysheva, M.N., Frolov, A.O., Yurchenko, V., Kostygov, A.Y. Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biol., 2023, 21(1): 191. PMID: 37697369

Klocek, D., Grybchuk, D., Macedo, D.H., Galan, A., Votýpka, J., Schmid-Hempel, R., Schmid-Hempel, P., Yurchenko, V., Kostygov, A.Y. RNA viruses of Crithidia bombi, a parasite of bumblebees. J. Invertebr. Pathol., 2023, 201: 107991. PMID: 37714407

Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol., 2024, 10(1): veae037. PMID: 38774311

Kostygov, A.Y., Grybchuk, D., Heeren, S., Gerasimov, E.S., Klocek, D., Reddy, A., Sádlová, J., Pacáková, L., Kohl, A., Stejskal, F., Volf, P., Dujardin, J.-C., Yurchenko, V. A novel strain of Leishmania braziliensis harbors not a toti- but a bunyavirus., PLoS Negl. Trop. Dis., 2024, 18(12): e0012767. PMID: 39729426

Grybchuk, D., Kostygov, A.Y., Yurchenko, V. Analysis of Leishbuviridae from trypanosomatids. In: Bunyaviruses: Methods and Protocols (Ed. H. Boshra), 2025, 2893: 151-167. ("Methods in Molecular Biology" Series v. 2893, Hardcover ISBN 978-1-0716-4337-2, Softcover ISBN 978-1-0716-4340-2, eBook ISBN 978-1-0716-4338-9, Series ISSN 1064-3745, Series E-ISSN 1940-6029). PMID: 39671036

Ingrid Škodová-Sveráková, Ph.D., postdoctoral researcher (part-time)

Education: Univerzita Komenského v Bratislave, Bratislava, Slovakia. Ph.D. 2014

Publications

Škodová-Sveráková, I.*, Záhonová, K.*, Bučková, B., Füssy, Z., Yurchenko, V., Lukeš, J. Catalase and ascorbate peroxidase in euglenozoan protists. Pathogens, 2020, 9: 317. * Equal contribution. PMID: 32344595

Zakharova, A., Albanaz, A.T.S., Opperdoes, F.R., Škodová-Sveráková, I., Zagirova, D., Saura, A., Chmelová, L’., Gerasimov, E.S., Leštinová, T., Bečvář, T., Sádlová, J., Volf, P., Lukeš, J., Horváth, A., Butenko, A., Yurchenko, V. Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content. PLoS Negl. Trop. Dis., 2022, 16(6): e0010510. PMID: 35749562

Opperdoes, F.R.*, Záhonová, K.*, Škodová-Sveráková, I.*, Bučková, B., Chmelová, L′., Lukeš, J., Yurchenko, V. In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics, 2024, 25(1): 184. * Equal contribution. PMID: 38365628

Chmelová, L′., Záhonová, K., Albanaz, A.T.S., Hrebenyk, L., Horváth, A., Yurchenko, V.*, Škodová-Sveráková, I.* Distribution and functional analysis of isocitrate dehydrogenases across kinetoplastids. Genome Biol. Evol., 2024, 16(3) evae042. * Co-correspondent authors. PMID: 38447055

Afonin, D.A., Gerasimov, E.S., Škodová-Sveráková, I., Záhonová, K., Gahura, O., Albanaz, A.T.S., Myšková, E., Bykova, A., Paris, Z., Lukeš, J., Opperdoes, F.R., Horváth, A., Zimmer, S.L., Yurchenko, V. Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucl. Acids Res., 2024, 52: 3870–3885. PMID: 38452217

Chmelová, L′., Kraeva, N., Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int. J. Parasitol., 2024, 54: 391-400. PMID: 38663543

Gerasimov, E.S., Afonin, D.A., Škodová-Sveráková, I., Saura, A., Trusina, N., Gahura, O., Zakharova, A., Butenko, A., Baráth, P., Horváth, A., Opperdoes, F.R., Pérez-Morga, D., Zimmer, S.L., Lukeš, J., Yurchenko, V. Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatid Vickermania. Proc. Natl. Acad. Sci. USA, 2025, 122(15): e2426887122. PMID: 40203041

PhD students

MSc. Arnau Galan Rigol, PhD student

Education: Universitat de Barcelona, Barcelona, Spain. MSc. 2021

Publications

Klocek, D., Grybchuk, D., Macedo, D.H., Galan, A., Votýpka, J., Schmid-Hempel, R., Schmid-Hempel, P., Yurchenko, V., Kostygov, A.Y. RNA viruses of Crithidia bombi, a parasite of bumblebees. J. Invertebr. Pathol., 2023, 201: 107991. PMID: 37714407

Chmelová, L′., Kraeva, N., Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int. J. Parasitol., 2024, 54: 391-400. PMID: 38663543

Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol., 2024, 10(1): veae037. PMID: 38774311

Záhonová, K., Füssy, Z., Albanaz, A., Butenko, A., Kachale, A., Kraeva, N., Galan, A., Zakharova, A., Stojanova, B., Votýpka, J., Kostygov, A.Y., Spodareva, V., Malysheva, M.N., Frolov, A.O., Rogozin, I., Paris, Z., Valasek, L., Yurchenko, V., Lukeš, J. Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio, 2025, (accepted). PMID:

Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A.Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. Converting Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code, into a genetically-tractable model. Mol. Microbiol., 2025, (accepted). PMID:

MSc. Donnamae Klocek

Education: Massey University, New Zealand. MSc. 2023

Publications

Saura, A., Zakharova, A., Klocek, D., Gerasimov, E.S., Butenko, A., Macedo, D.H., Servienė, E., Zagirova, D., Meshcheryakova, A., Rogozin, I.B., Serva, S., Kostygov, A.Y., Yurchenko, V. Elimination of LRVs elicits different responses in Leishmania spp. mSphere, 2022, 7(4): e00335-22. PMID: 35943162

Klocek, D., Grybchuk, D., Tichá, L., Votýpka, J., Volf, P., Kostygov, A.Y., Yurchenko, V. Evolution of RNA viruses in trypanosomatids: new insights from the analysis of Sauroleishmania. Parasitol. Res., 2023, 122(10): 2279-2286. PMID: 37490143

Macedo, D.H., Grybchuk, D., Režnarová, J., Votýpka, J., Klocek, D., Yurchenko, T., Ševčík, J., Magri, A., Urda Dolinská, M., Záhonová, K., Lukeš, J., Servienė, E., Jászayová, A., Serva, S., Malysheva, M.N., Frolov, A.O., Yurchenko, V., Kostygov, A.Y. Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biol., 2023, 21(1): 191. PMID: 37697369

Rêgo, F.D., da Silva, E.S., Lopes, V.V., Teixeira-Neto, R.G., Belo, V.S., Fonseca Júnior, A.A., Pereira, D.A., Pena, H.P., Laurenti, M.D., Flores, G.V.A., da Matta, V.L.R., Chouman, I.H., Burrin, T.B., Pacheco, C.M.S., Barrouin-Melo, S.M., de Pinho, F.A., de Andrade, H.A., Nunes, R.V., Gontijo, C.M.F., Soccol, V.T., Klocek, D., Grybchuk, D., Macedo, D.H., do Monte-Neto, R.L., Yurchenko, V., Soares, R.P. First report of putative Leishmania RNA virus 2 (LRV2) in Leishmania infantum strains from canine and human visceral leishmaniasis cases in the Southeast of Brazil. Mem. Inst. Oswaldo Cruz, 2023, 118: e230071. PMID: 37729273

Klocek, D., Grybchuk, D., Macedo, D.H., Galan, A., Votýpka, J., Schmid-Hempel, R., Schmid-Hempel, P., Yurchenko, V., Kostygov, A.Y. RNA viruses of Crithidia bombi, a parasite of bumblebees. J. Invertebr. Pathol., 2023, 201: 107991. PMID: 37714407

Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol., 2024, 10(1): veae037. PMID: 38774311

Kostygov, A.Y., Grybchuk, D., Heeren, S., Gerasimov, E.S., Klocek, D., Reddy, A., Sádlová, J., Pacáková, L., Kohl, A., Stejskal, F., Volf, P., Dujardin, J.-C., Yurchenko, V. A novel strain of Leishmania braziliensis harbors not a toti- but a bunyavirus., PLoS Negl. Trop. Dis., 2024, 18(12): e0012767. PMID: 39729426

MSc. Elora Kalita

Education: Central University of Rajasthan, Ajmer, India. MSc. 2022

Publications

Kostygov, A.Y., Skýpalová, K., Kraeva, N., Kalita, E., McLeod, C., Yurchenko, V., Field, M.C., Lukeš, J., Butenko, A. Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol., 22, 281. PMID: 39627879

Mgr. Karolína Skýpalová (under tutelage of Dr. Kostygov)

Education: Ostravská Univerzita, Ostrava, Czech Republic. Mgr. 2023

Publications

Zavataro, A.L.E.*, Skýpalová, K.*, Vergara, P.O.T., Silva, F.M, Butenko, A., Yurchenko, V., Kostygov, A.Y., Alves, J.M.P. The genome of the endosymbiont-harboring trypanosomatid Kentomonas sorsogonicus. Protistology, 2024, 18(1): 72-81. * Equal contribution.

Kostygov, A.Y.*, Skýpalová, K.*, Kraeva, N., Kalita, E., McLeod, C., Yurchenko, V., Field, M.C., Lukeš, J., Butenko, A. Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol., 22, 281. * Equal contribution. PMID: 39627879

MSc. Aditya Reddy

Education: Central University of Kerala, India. MSc. 2019

Publications

Kostygov, A.Y., Grybchuk, D., Heeren, S., Gerasimov, E.S., Klocek, D., Reddy, A., Sádlová, J., Pacáková, L., Kohl, A., Stejskal, F., Volf, P., Dujardin, J.-C., Yurchenko, V. A novel strain of Leishmania braziliensis harbors not a toti- but a bunyavirus., PLoS Negl. Trop. Dis., 2024, 18(12): e0012767. PMID: 39729426

MSc. Kate Obaayaa Sagoe

Education: Pan African University Institute for Basic Sciences, Technology and Innovation, Kenya. MSc. 2023

MSc. Eva Andrea Dueñas Villavicencio

Education: Universidad Peruana Cayetano Heredia, Peru. MSc. 2022

Lab alumni, postdocs

Dr. Aleksander Losev

2015

Dr. Claretta Bianchi

2022

Lab alumni, Ph.D. students

Dr. Natalya Kraeva

2017, Ph.D. thesis: "Analysis of genetic differences between monoxenous and dixenous Leishmaniinae for identification of novel virulence factors"

Dr. Anastasiia Grybchuk-Ieremenko

2017, Ph.D. thesis: "Diversity and molecular phylogeny of monoxenous insect trypanosomatids and trypanosomes from freshwater vertebrates"

Dr. Aygul Ishemgulova

2017, Ph.D. thesis: "Functional genomics of Leishmania virulence"

Dr. Danyil Grybchuk

2017, Ph.D. thesis: "Diversity and phylogeny of RNA viruses in Trypanosomatidae with insights into viral ecology and host cell interaction"

Dr. Lucie Podešvová

2020, Ph.D. thesis: "The new molecular tools for Leishmania research"

Dr. Diego Henrique Fagundes Macedo

2021, Ph.D. thesis: "Jumping on the viral bandwagon: a study on the diversity and evolution of RNA viruses in trypanosomatids with the emphasis on leishmaniaviruses"

Dr. Jana Režnarová (Králová) (supervised by Dr. Alexei Kostygov)

2021, Ph.D. thesis: "Diversity and biology of monoxenous trypanosomatids on a broad and specific scale"

Dr. Arzuv Charyyeva

2021, Ph.D. thesis: "Leishmania virulence: from haplotype network to functional genomics"

Dr. Claretta Bianchi

2022, Ph.D. thesis: "Catalase: what happened in the evolution of Trypanosomatidae?"

Dr. Alexandra Zakharova

2023, Ph.D. thesis: "The inner society of endosymbionts in Leishmaniinae"

Dr. Amanda Albanaz

2023, Ph.D. thesis: "Comparative genomics of Trypanosomatidae: from model organisms to outliers"

Dr. Anastasiia Bykova

2024, Ph.D. thesis: "The role of various types of mutations in evolution of SARS-CoV genomes"

Dr. Ľubomíra Chmelová

2024, Ph.D. thesis: "Insights into biochemistry of trypanosomatids"

Lab alumni, MSc. students

Mgr. Lucie Kortišová, 2015

Mgr. Dalibor Váhala, 2015

Mgr. Denisa Mlacovská, 2017

Mgr. Adriana Volná, 2017

Mgr. Martin Kovačik, 2018

Mgr. Alena Dembitskaya, 2019

Mgr. Sabina Kühnelová, 2019 (supervised by Dr. Alexei Kostygov)

Mgr. Sandra Warmusová, 2022

Mgr. Adam Krayzel, 2023 (supervised by Dr. Natalya Kraeva)

Mgr. Martina Byrtusová, 2024 (supervised by Dr. Natalya Kraeva)