Obornik Lab

Laboratory of molecular taxonomy (M.Obornik)

The Laboratory of Molecular Taxonomy (LMT) was established in 2000 as a joint project of the Institute of Parasitology and Faculty of Biological Sciences, University of South Bohemia. The laboratory is designed to study molecular evolution of single celled eukaryotes, mainly those that have been involved in the process of secondary endosymbiosis. LMT is supported by the Ministry of Education (CEZ AJ06/98 F1-123100003) and grants covering particular projects.

Novel protists from corals

The novel group of photosynthetic alveolates was isolated from the stony corals by Robert Moore (now at University Syndey, Australia). In collaboration, we are working on their molecular characterization and phylogeny, as well as characterization of their organelles. The novel alga was named Chromera velia and represents a novel phylum Chromerida within Alveolata.

Diatom genomics

Many unicellular photoautotrophic eukaryotes (e.g. diatoms, heterokonts, cryptophytes, haptophytes, dinoflagellates, euglenoids) possess complex chloroplasts that evolved during the process of secondary endosymbiogenesis. The staff of LMT have participated in the annotation of the genome of centric diatom Thalassiosira pseudonana, particularly in the search of nuclear-encoded plastid targeted proteins, and their in silico characterisation and phylogeny. Recently, two staff members have been invited to participate in the annotation of the genome of the pennate diatom Phaeodactylum tricornutum.

Mosaic biosynthetic pathways and evolution of eukaryotes

During the first diatom genome project we have analyzed several plastid-located metabolic pathways. Surprisingly, not all nuclear-encoded plastid-targeted proteins are of cyanobacterial (plastid) origin. It is obvious that chloroplasts can utilize enzymes that are not of a cyanobacterial origin. We have shown that nuclear-encoded cyanobacterial enzymes can be replaced by their cytosolic or mitochondrial counterparts, ultimately to be incorporated into the metabolism of the chloroplast. It is evident that composition and location of some pathways were deeply influenced by the process of secondary endosymbiosis.

Apicomplexan parasites of invertebrates

Evolution and phylogenetic relationships of apicomplexan parasites have been intensively studied. However, research has been focused on those parasitizing humans or animals with high economical importance. This led to the unbalanced taxon sampling affecting phylogenetic analyses, which have not so far contained coccidia from invertebrate hosts. We sequenced SSU rRNA genes from several coccidians from invertebrate hosts, particularly insects (apicomplexans of the genus Adelina) and cephalopods (the apicomplexan genus Aggregata) and investigated their phylogenetic relationships. This work was done (M.O.) in long-term collaboration with David Modrý (Veterinary University Brno).



Articles in press

41. Oborník M, Modrý D, Lukeš M, Černotíková-Stříbrná E, Cihlář J, Tesařová M, Kotabová E, Vancová M, Prášil O, Lukeš J. (2012) Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef. Protist accepted

40. Kořený L, Sobotka R, Janouškovec J, Keeling PJ, Oborník M (2011) Tetrapyrrole synthesis of photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites. Plant Cell accepted

39. Valenčáková A, Balent P, Ravaszová P, Horák A, Oborník M, Halanová M, Malčeková M, Novotný F, Goldová M (2011) Molecular identification and genotyping of microsporidia in selected hosts. Parasitology Research DOI 10.1007/s00436-011-2543-9 (in press)


38. Allen AE, Dupont CL, Oborník M, Horák A, Nunes-Nesi A, McCrow JP, Zheng H, Johnson DA, Hu H, Fernie AR, Bowler C (2011) Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature 473, 203-207.

37. Kořený L, Oborník M. (2011) Sequence evidence for the presence of two tetrapyrrole pathways in Euglena gracilis. Genome Biology and Evolution 3, 359-364.

36. Borovička J, Noordeloos ME, Gryndler M, Oborník M. (2010) Molecular phylogeny of Psilocybe cyanescens complex in Europe, with reference to the position of the secotioid Weraroa novae-zelandiae. Mycological Progress 10, 149-155

35. Oborník M, Vancová M, Lai DH, Janouškovec J, Keeling PJ, Lukeš J. (2011) Morphology and ultrastructure of multiple life cycle stages of the photosynthetic relative of apicomplexa, Chromera velia. Protist 162, 115-130


34. Jiroutová K, Kořený L, Bowler C, Oborník M. (2010) A Gene in the Process of Endosymbiotic Transfer. PLoS ONE 5, e13234

33. Janouškovec J, Horák A, Oborník M, Lukeš J, Keeling PJ (2010) A common red algal origin of the apicomplexan, dinoflagellate and heterokont plastids. Proceedings of the National Academy of Sciences of USA 107, 10949-10954

32. Kořený L, Lukeš J, Oborník M (2010) Evolution of the heme synthetic pathway in kinetoplastid flagellates: An essential pathway that is not essential after all? International Journal for Parasitology 40, 149-156

31. Poliak P, Van Hoewyk D, Oborník M,, Zíková A, Stuart KD, Tachezy J, Pilon M, Lukes J (2010)Functions and cellular localization, of cysteine desulphurase and selenocystein lyase in Trypanosoma brucei. FEBS Journal 277, 383-393


30. Miloslav Jirků, Milan Jirků, Oborník M., Lukeš J., Modrý D. (2009) Goussia Labbé, 1896 (Apicomplexa, Eimeriorina) in Amphibia: Diversity, Biology, Molecular Phylogeny and Comments on the Status of the Genus. Protist 160, 123-136.

29. Jirků M., Jirků M., Lukeš J., Oborník M., Petrželková K., Modrý D. (2009) A model for taxonomic work on homoxenous coccidia: redescription, host specificity, and molecular phylogeny of Eimeria ranae Dobell, 1909, with critical review of Eimeria spp. parasitizing anuran hosts. Journal of Eukaryotic Microbiology 56, 39-51.

28. Oborník M (2009) Identification and Diagnostics of Entomopathogenic Protozoa. in: SP Stock, J Vandenberg, I Glazer and Boemare N, (eds.) Insects Pathogens: Molecular Approaches and Techniques, CAB International, 101-128. (book chapter)

27. Oborník M (2009) Endosymbiosis as an accelerator of evolution (Endosymbióza jako akcelerátor evoluce). Živa 2/2009, 50-52. (invited review in Czech)

26. Oborník M., Janouškovec J., Chrudimský T., Lukeš J. (2009) Evolution of the apicoplast and its hosts: from heterotrophy to autotrophy and back again. International Journal for Parasitology 39, 1-12. (invited review)


25. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret J-P, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJJ, Jenkins BD, Jiroutová K, Jorgensen RE, Joubert Y, Kaplan A, Kröger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin–Jézéquel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot–Le Secq M-P, Napoli C, Oborník M, Schnitzler Parker M, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456, 239-244.

24. Coesel S, Oborník M, Varela J, Falciatore A, Bowler C (2008) Evolutionary Origins and Functions of the Carotenoid Biosynthetic Pathway in Marine Diatoms. PLoS ONE 3: e2896

23. Moore RB, Oborník M, Janouškovec J, Chrudimský T, Vancová M, Green DH, Wright SW, Davies NW, Bolch CJS, Heimann K, Šlapeta J, Hoegh-Guldberg O, Logsdon JM, Carter DA. (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451, 959-963.


22. Jiroutová K, Horák A, Bowler C, Oborník M (2007) Tryptophan Biosynthesis in Stramenopiles: Eukaryotic Winners in the Diatom Complex Chloroplast. Journal of Molecular Evolution 65, 496-511

21. Hyliš M, Oborník M, Nebesářová J, Vávra J (2007) Aquatic tetrasporoblastic microsporidia from caddis flies (Insecta, Trichoptera): Characterization, phylogeny and taxonomic reevaluation of the genera Episetum Larsson, 1986, Pyrotheca, Hesse, 1935 and Cougourdella Hesse, 1935. European Journal of Protistology 43, 205-224

20. Lukeš J, Mauricio IL, Schönian G, Dujardin JC, Soteriadou K, Dedet JP, Kuhls K, Tintaya KWQ, Jirků M, Chocholová E. Haralambous C, Pratlong F, Oborník M, Horák A, Ayala FJ, Miles MJ (2007) Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proceedings of the National Academy of Sciences of USA 104: 9375-9380

19. Svobodová M, Zídková L, Čepička I, Oborník M, Lukeš J and Votýpka J (2007) Sergeia podlipaevi gen. nov., sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of biting midges (Ceratopogonidae, Diptera). International Journal of Systematic and Evolutionary Microbiology 57: 423-432


18. Kopečná J, Jirku M, Oborník M, Tokarev YS, Lukeš J, Modrý D (2006) Phylogenetic analysis of coccidian parasites from invertebrates: Search for missing links. Protist 157:173-183

17. Macháčková M, Oborník M, Kopecký J (2006) Effect of salivary gland extract from Ixodes ricinus ticks on the proliferation of Borrelia burgdorferi sensu stricto in vivo. Folia Parasitologica 53:153-158

16. Hyliš M, Pilarska DK, Oborník M, Vávra J, Solter LF, Weiser J, Linde A, McManus ML (2006) Nosema chrysorrhoeae n. sp (Microsporidia), isolated from browntail moth (Euproctis chrysorrhoea L.) (Lepidoptera, Lymantriidae) in Bulgaria: Characterization and phylogenetic relationships. Journal of Invertebrate Pathology 91:105-114


15. Oborník M, Green BR (2005) Mosaic Origin of the Heme Biosynthesis Pathway in Photosynthetic Eukaryotes. Molecular Biology and Evolution 22 : (11) 1-11

14. Ležalová R, Tkadlec E, Oborník M, Šimek J, Honza M (2005) Should males come first? The relationship between offspring hatching order and sex in the black-headed gull Larus ridibundus. Journal of Avian Biology 36:478-483

13. Hyliš M, Weiser J, Oborník M, Vávra J (2005) DNA isolation from museum and type collection slides of microsporidia. Journal of Invertebrate Pathology 88 (3): 257-260

12. Vávra J , Hyliš M , Oborník M, Vossbrinck CR (2005) Microsporidia in aquatic microcrustacea: the copepod microsporidium Marssoniella elegans Lemmermann, 1900 revisited. Folia Parasitologica 52: 163-172


11. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WWY, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Oborník M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson PF, Rokhsar, DS (2004) The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306: 79-86

10. Votýpka J, Lukeš J, Oborník M (2004) Phylogenetic relationship of Trypanosoma corvi with other avian trypanosomes. Acta Protozoologica 43: 225-231


9. Oborník M, Van de Peer Y, Hypša V, Frickey T, Šlapeta JR, Meyer A, Lukeš J (2002) Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast. Gene 285: 109-118.

8. Oborník M, Jirku M, Šlapeta JR, Modrý D, Koudela B, Lukeš J (2002) Notes on coccidian phylogeny based on the apicoplast small subunit ribosomal DNA. Parasitology Research 88: 360-363.

7. Votýpka J, Oborník M, Volf P, Svobodová M, Lukeš J (2002) Trypanosoma avium of raptors (Falconiformes:) Phylogeny and identification of vectors. Parasitology 125: 253-263.


6. Dyková I, Kyselová I, Pecková H, Oborník M, Lukeš J (2001) Identity of Naegleria strains isolated from organs of freshwater fishes. Diseases of Aquatic Organisms 46: 115-121.

5. Šlapeta JR, Modrý D, Votýpka J, Jirku M, Oborník M, Lukeš J, Koudela B (2001) Eimeria telekii n. sp. (Apicomplexa: Coccidia) from Lemniscomys striatus (Rodentia: Muridae): morphology, pathology and phylogeny. Parasitology 122: 133-143.

4. Oborník M, Jirku M, Doležel D (2001) Phylogeny of mitosporic entomopathogenic fungi: is the genus Paecilomyces polyphyletic? Canadian Journal of Microbiology 47: 813-819.

3. Modrý D, Šlapeta JR, Jirku M, Oborník M, Lukeš J, Koudela B (2001) Phylogenetic position of a renal coccidium of the European green frogs, 'Isospora' lieberkuehni Labbe 1894 (Apicomplexa: Sarcocystidae) and its taxonomic implications. International Journal of Systematic and Evolutionary Microbiology 51: 767-772.


2. Oborník M, Klíč M, Žižka L (2000) Genetic variability and phylogeny inferred from random amplified polymorphic DNA data reflect life strategy of entomopathogenic fungi. Canadian Journal of Botany 78: 1150-1155.


1. Doležel D, Koudela B, Jirku M, Hypša V, Oborník M, Votýpka J, Modrý D, Šlapeta JR, Lukeš J (1999) Phylogenetic analysis of Sarcocystis spp. of mammals and reptiles supports the coevolution of Sarcocystis spp. with their final hosts. International Journal for Parasitology 29 : 795-798.





List of people of Laboratory: Obornik Lab



List of publications of Laboratory: Obornik Lab