Marek Eliáš - publications

papers in peer-reviewed journals, book chapters:

2016

Yurchenko T, Ševčíková T, Strnad H, Butenko A and Eliáš M (2016) The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite. Open Biology, accepted pending minor revisions.

Záhonová K, Kostygov A, Ševčíková T, Yurchenko V and Eliáš M (2016) An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons. Current Biology 27:2364–2369.

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

Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavin JL, Lee SC, Li W, Lindquist E, López-García S, Luque E, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez RM, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martinez S, Idnurm A, Herrera-Estrella A, Gabaldón T and Grigoriev IV (2016) Expansion of signal transduction pathways in fungi by extensive genome duplication. Current Biology 26:1577–1584.

Karnkowska A, Vacek V, Zubáčová Z, Treitli S, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č and Hampl V (2016) A eukaryote without a mitochondrial organelle. Current Biology 26:1274–1284.

Flegontov P, Butenko A, Firsov S, Kraeva N, Eliáš M, Field MC, Filatov D, Flegontova O, Gerasimov ES, Hlaváčová J,  Ishemgulova A, Jackson AP, Kelly S, Kostygov AY, Logacheva MD, Maslov D, Opperdoes FR, O'Reilly A, Sádlová J, Ševčíková T, Venkatesh D, Vlček C, Volf P, Votýpka J, Záhonová K, Yurchenko V and Lukeš J (2016) Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Scientific Reports 6:23704.

Ševčíková T, Zbránková Z, Klimeš V, Strnad H, Hroudová M, Vlček Č and Eliáš M (2016) A comparative analysis of mitochondrial genomes in eustigmatophyte algae. Genome Biology and Evolution 8:705–722.

Eliáš M, Klimeš V, Derelle R, Petrželková R and Tachezy J (2016) A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution. Biology Direct 11:5.

2015

Ševčíková T, Horák A, Klimeš V, Zbránková V, Demir-Hilton E, Sudek S, Jenkins J, Schmutz J, Přibyl P, Fousek J, Vlček Č, Lang BF, Oborník M, Worden AZ and Eliáš M (2015) Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Scientific Reports 5:10134.

Speijer D, Lukeš J and Eliáš M (2015) Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. Proceedings of the National Academy of Sciences of the United States of America 112:88278834.

Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P and Roger AJ (2015) An ancestral bacterial division system is widespread in eukaryotic mitochondria. Proceedings of the National Academy of Sciences of the United States of America 112:1023910246.

Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF and Eliáš M (2015) Bacterial proteins pinpoint a single eukaryotic root. Proceedings of the National Academy of Sciences of the United States of America 112:E693–E699.

2014

Petrželková R and Eliáš M (2014) Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida. Acta Societatis Botanicorum Poloniae 83:303–315.

Klimeš V, Gentekaki E, Roger AJ and Eliáš M (2014) A large number of nuclear genes in the human parasite Blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biology and Evolution 6:1956–1961.

Fawley KP, Eliáš M, Fawley MW (2014) The diversity and phylogeny of the commercially important algal class Eustigmatophyceae, including the new clade Goniochloridales. Journal of Applied Phycology 26:1773–1782.

Vukašinović N, Cvrčková F, Eliáš M, Cole R, Fowler JE, Žárský V and Synek L (2014) Dissecting a Hidden Gene Duplication: the Arabidopsis thaliana SEC10 Locus. PLoS ONE 9:e94077.

Záhonová K, Hadariová L, Vacula R, Yurchenko V, Eliáš M, Krajčovič J and Vesteg M (2014) A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis. FEBS Letters 588:783–788.

2013

Kaufnerová V and Eliáš M (2013) The demise of the genus Scotiellopsis Vinatzer (Chlorophyta). Nova Hedwigia 97:415–428.

Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, Herman EK, Lin YC, Napier J, Ogata H, Sarno AF, Shmutz J, Schroeder D, de Vargas C, Verret F, von Dassow P, Valentin K, Van de Peer Y, Wheeler G; Emiliania huxleyi Annotation Consortium (incl. Eliáš M), Dacks JB, Delwiche CF, Dyhrman ST, Glöckner G, John U, Richards T, Worden AZ, Zhang X and Grigoriev IV (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499:209–213.

Gaysina L, Němcová Y, Škaloud P, Ševčíková T and Eliáš M (2013) Chloropyrula uraliensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a new green coccoid alga with a unique ultrastructure, isolated from soil in South Urals. Journal of Systematics and Evolution 51:476–484.

Schlacht A, Mowbrey K, Elias M, Kahn RA and Dacks JB (2013) Ancient complexity, opisthokont plasticity, and discovery of the 11th subfamily of Arf GAP proteins. Traffic 14:636–649.

Collén J, Porcel B, Carré W, Ball S, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K, Elias M, Artiguenave F, Arun A, Aury JM, Barbosa-Neto JF, Bothwell JH, Bouget FY, Brillet L, Cabello-Hurtado F, Capella-Gutíerrez S, Charrier B, Cladiere L, Cock JM, Coelho SM, Colleoni C, Czjzek M, Da Silva C, Delage L, Denoeud F, Deschamps F, Dittami SM, Gabaldón T, Gachon CMM, Groisillier A, Hervé C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, Leblanc C, Lopez PJ, McLachlan D, Meslet-Cladiere L, Moustafa A, Nehr Z, Nyval-Collén P, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Weissenbach J, Zambounis A, Wincker P and Boyen C (2013) Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proceedings of the National Academy of Sciences of the United States of America 110:5247–5252.

Fulnečková J, Ševčíková T, Fajkus J, Lukešová A, Lukeš M, Vlček Č, Lang BF, Kim E, Eliáš M and Sýkorová E (2013) A broad phylogenetic survey unveils the diversity and evolution of telomeres in eukaryotes. Genome Biology and Evolution 5:468–483.

Eliáš M, Neustupa J, Pažoutová M and Škaloud P (2013) A case of taxonomic inflation in coccoid algae: Ellipsoidion parvum and Neocystis vischeri are conspecific with Neocystis (=Nephrodiella) brevis (Chlorophyta, Trebouxiophyceae). Phytotaxa 76:15–27.

2012

Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJM, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale C, Hempel F, Henrissat B, Höppner MP, Ishida KI, Kim E, Kořený L, Kroth PG, Liu Y, Malik SH, Maier UG, McRose D, Mock T, Neilson JAD, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV and Archibald JM (2012) Algal nuclear genomes reveal evolutionary mosaicism and fate of nucleomorphs. Nature 492:59–65.

Cock JM, Sterck L, Ahmed S, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Arun A, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corguillé GL, Corre E, Dartevelle L, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CMM, Godfroy O, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Luthringer R, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Macaisne N, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Scornet D, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, Von Dassow P, Yamagishi T, Rouzé P, Van De Peer Y and Wincker P (2012) The Ectocarpus Genome and Brown Algal Genomics. Advances in Botanical Research 64:141–184.

Elias M, Brighouse A, Gabernet-Castello C, Field MC and Dacks JB (2012) Sculpting the endomembrane system in deep time: High resolution phylogenetics of Rab GTPases. Journal of Cell Science 125:2500–2508.

Fulnečková J, Hasíková T, Fajkus J, Lukešová A, Eliáš M and Sýkorová E (2012) Dynamic evolution of telomeric sequences in the green algal order Chlamydomonadales. Genome Biology and Evolution 4:248–264.

Zambounis A, Elias M, Sterck L, Maumus F and Gachon CMM (2012) Highly dynamic exon shuffling in candidate pathogen receptors...What if brown algae were capable of adaptive immunity? Molecular Biology and Evolution 29:1263–1276.

Přibyl P, Eliáš M, Cepák V, Lukavský J and Kaštánek P (2012) Zoosporogenesis, morphology, ultrastructure, pigment composition, and phylogenetic position of Trachydiscus minutus (Eustigmatophyceae, Heterokontophyta). Journal of Phycology 48:231–242.

Eliáš M and Klimeš V (2012) Rho GTPases: deciphering the evolutionary history of a complex protein family. Methods in Molecular Biology 827:13–34.

2011

Němcová Y, Eliáš M, Škaloud P, Neustupa J and Hodač L (2011) Jenufa gen. nov., a new genus of coccoid green algae (Chlorophyceae, incertae sedis) previously recorded by environmental sequencing. Journal of Phycology 47:928–938.

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, Depamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, Debarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga SI, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riano-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sorensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theißen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D and Grigoriev IV (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960–963.

Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Madan Babu M, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm R, Shaulsky G, Strassmann JE, Queller DC, Kuspa A and Grigoriev I (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology 12:R20.

Vlahou G, Elias M, von Kleist-Retzow JC, Wiesner RJ and Rivero F (2011) Non-metazoan Ras related GTPases of the Miro family are not required for mitochondrial transport: functional analysis of the Dictyostelium discoideum ortholog. European Journal of Cell Biology 90:342–355.

Neustupa J, Eliáš M, Škaloud P, Němcová Y and Šejnohová L (2011) Xylochloris irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga. Phycologia 50: 57–66.

2010

Elias M (2010) Patterns and processes in the evolution of the eukaryotic endomembrane system. Molecular Membrane Biology 27:469–489.

Cock JM, Porcel B, Carré W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K, Elias M, Artiguenave F, Arun A, Aury JM, Barbosa-Neto JF, Bothwell JH, Bouget FY, Brillet L, Cabello-Hurtado F, Capella-Gutiérrez S, Charrier B, Cladière L, Cock JM, Coelho SM, Colleoni C, Czjzek M, Da Silva C, Delage L, Denoeud F, Deschamps P, Dittami SM, Gabaldón T, Gachon CM, Groisillier A, Hervé C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, Leblanc C, Lopez PJ, McLachlan DH, Meslet-Cladiere L, Moustafa A, Nehr Z, Nyvall Collén P, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Weissenbach J, Zambounis A, Wincker P and Boyen C (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465:617–621.

Eliáš M, Němcová Y, Škaloud P, Neustupa J, Kaufnerová V and Šejnohová L (2010) Hylodesmus singaporensis gen. et sp. nov., a new autosporine subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore. International Journal of Systematic and Evolutionary Microbiology 60:1224–1235.

2009

Elias M and Archibald JM (2009) Sizing up the genomic footprint of endosymbiosis. BioEssays 31:1273–1279.

Eliáš M and Neustupa J (2009) Pseudomarvania gen. nov. (Chlorophyta, Trebouxiophyceae), a new genus for the “budding” subaerial green algae Marvania aerophytica Neustupa & Šejnohová and Stichococcus ampulliformis Handa. Fottea 9:169–177.

Neustupa J, Němcová Y, Eliáš M and Škaloud P (2009) Kalinella bambusicola gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid Chlorella-like subaerial alga from Southeast Asia. Phycological Research 57:159–169.

Elias M, Patron NJ and Keeling PJ (2009) The RAB Family GTPase Rab1A from Plasmodium falciparum Defines a Unique Paralog Shared by Chromalveolates and Rhizaria. Journal of Eukaryotic Microbiology 56:348–356.

Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O’Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA and Wickes BL (2009) Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genetics 5:e1000549.

Elias M and Archibald JM (2009) The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus. Gene 442:63–72.

2008

Eliáš M, Škaloud P and Neustupa J (2008) Elliptochloris bilobata var. corticola var. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccal green alga. Biologia 63:787–794.

Elias M (2008) The guanine nucleotide exchange factors Sec2 and PRONE: candidate synapomorphies for the Opisthokonta and the Archaeplastida. Molecular Biology and Evolution 25:1526–1529.

Elias M and Novotny M (2008) cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution. Biology Direct 3:21.

2007

Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245–250.

Neustupa J, Eliáš M and Šejnohová L (2007) A taxonomic study of two Stichococcus (Trebouxiophyceae, Chlorophyta) species with a starch-enveloped pyrenoid. Nova Hedwigia 84:51–63.

2006

Synek L, Schlager N, Eliáš M, Quentin M, Hauser MT and Žárský V (2006) AtEXO70A1, a member of a family of putative exocyst subunits specifically expanded in land plants, is important for polar growth and plant development. Plant Journal 48:54–72.

Kahn RA, Cherfils J, Elias M, Lovering R, Munro S, Schurmann A (2006) Nomenclature for the human Arf family of GTP-binding proteins: ARF, ARL, and SAR proteins. Journal of Cell Biology 172:645–650.

Before 2006

Hála M, Eliáš M and Žárský V (2005) A specific feature of the angiosperm Rab escort protein (REP) and evolution of the REP/GDI superfamily. Journal of Molecular Biology 348:12991313.

Eliáš M, Drdová E, Žiak D, Bavlnka B, Hála M, Cvrčková F, Soukupová H and Žárský V (2003) The exocyst complex in plants. Cell Biology International 27:199–201.

Potocký M, Eliáš M, Profotová B, Novotná Z, Valentová O and Žárský V (2003) Phosphatidic acid produced by phospholipase D is required for tobacco pollen tube growth. Planta 217:122–130.

Eliáš M, Potocký M, Cvrčková F and Žárský V (2002) Molecular Diversity of Phospholipase D in Angiosperms. BMC Genomics 3:2.

Eliáš M, Cvrčková F, Obermeyer G and Žárský V (2001) Microinjection of Guanine Nucleotide Analogues into Lily Pollen Tubes Results in Isodiametric Tip Expansion. Plant Biology 3:489–492.

Cvrčková F, Eliáš M, Hála M, Obermeyer G and Žárský V (2001) Small GTPases and conserved signalling pathways in plant cell morphogenesis: from exocytosis to the Exocyst. In: A. Geitmann and I. Brent Heath (eds.), Cell Biology of Plant and Fungal Tip Growth, IOS Press, Amsterdam, 2001.