Publications
Peer-reviewed journals
2024
[56] van Hooff JJE, Raas MWD, Tromer EC, Eme L. Shaping up genomes: Prokaryotic roots and eukaryotic diversification of SMC complexes. Submitted.
[55] Baker BA, Gutierrez-Preciado A, Rodriguez del Rio A, McCarthy C, Lopez-Garcia P, Huerta-Cepas J, Susko E, Roger AJ, Eme L*, Moreira D*. Several independent adaptations of archaea to hypersaline environments.
Nature Microbiology (in press). *Co-corresponding author
2023
[55] Tahon G, Köstlbacher S, Pelve EA, Baker BJ, Saw JH, Eme L, Tamarit D, Schön ME, Ettema TJG Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching. Resubmitted after revisions.
[54] Blaz J, Galindo LJ, Heiss AA, Kaur H, Torruella G, Yang A, Thompson A, Filbert A, Warring S, Narechania A, Shiratori T, Ishida K-I, Dacks JB, López-García P, Moreira D, Kim E, Eme L. High-quality genome and transcriptome data for two new species of Mantamonas, a deep-branching eukaryote clade.
Scientific Data 10 (1), 603
[53] Yubuki N, Torruella G, Galindo LJ, Heiss AA, Ciobanu MC, Shiratori T, Ishida K-I, Blaz J, Kim E, Moreira D, López-García P, Eme L. Molecular and morphological characterisation of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida.
J Euk Micro
[52] Novák LVF, Treitli SC, Pyrih J, Shweta V, Vacek V, Brzoň O, Soukal P, Eme L, Dacks JB, Karnkowska A, Eliáš M, Hampl V. Genomics of Preaxostyla Flagellates Illuminates Evolutionary Transitions and the Path Towards Mitochondrial Loss.
Plos Genetics 19 (12), e1011050 2023.
[51] van Hooff JJE, Eme L. Lateral gene transfer leaves lasting traces in Rhizaria. BiorXiv.
[50] Eme L, Tamarit D, Caceres EF, Stairs C, de Anda V, Schon M-E, Seitz K, Dombrowski N, Lewis WH, Saw JH, […], Ettema TJG. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.
Nature (2023): 1-8.
2022
[49] Eme L, Stairs CW. Life through the lens of metabolism. (Book review).
Nature Ecology and Evolution (2022).
[48] Tamarit D, Caceres E, Krupovic M, Nijland R, Eme L, , . A closed Candidatus Odinarchaeum genome exposes Asgard archaeal viruses.
Nature Microbiology (2022) 7 (7), 948-952.
[47] van Beveren F, Eme L, López-García P, Ciobanu M, Moreira D. Independent Size Expansions and Intron Proliferation in Red Algal Plastid and Mitochondrial Genomes.
Genome biology and evolution. 2022 Apr;14(4):evac037.
[46] Zhang X, Hu Y, Eme L, Maruyama S, Eveleigh RJ, Curtis BA, Sibbald SJ, Hopkins JF, Filloramo GV, van Wijk KJ, Archibald JM. TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.
STAR protocols. 2022 Mar 18;3(1):101175.
[45] Munoz-Gomez S, Susko E, Williamson K, Eme L, Slamovits C, Moreira M, Lopez-Garcia P, Roger AJR. A site-and-branch-heterogeneous model on an expanded dataset favor mitochondria as sister to known Alphaproteobacteria.
Nature Ecology & Evolution, volume 6, pages 253-262 (2022).
2021
[44] Stairs CW, Taborský P, Salomaki ED, Kolisko M, Panek T, Eme L, Hradilov M, Vlček C, Jerlstrom-Hultqvist J, Roger AJ, Čepička I. Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes.
Current Biology.
[43] Tice AK, Žihala D, Pánek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
PLoS biology. 2021 Aug 6;19(8):e3001365.
[42] Koreny L, Zeeshan M, Barylyuk K, Tromer EC, van Hooff JJE, Brady D, Ke H, Chelaghma S, Ferguson DJP, Eme L, Tewari R, Ross F Waller. Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species.
PLoS biology, 19(3), e3001081
[41] Žárský V, Klimeš V, Pačes J, Vlček Č, Nývltová E, Hrdý I, Pyrih J, Mach J, Barlow L, Eliáš M, Dacks J, Hall N, Stairs CW, Eme L, Roger AJ, Tachezy J Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba.
Molecular Biology and Evolution, 38 (6), 2240-2259.
2020
[40] Salomaki E, Eme L, Brown MW, Kolisko M. Releasing uncurated datasets is essential for reproducible phylogenomics.
Nature Ecology and Evolution, 1-3.
[39] Sibbald SJ, Eme L, Archibald JM, Roger AJ. Lateral gene transfer mechanisms and pan-genomes in eukaryotes.
Trends in Parasitology, 19 Aug 2020, 36(11):927-941
[38] Stairs CW*, Dharamshi JE*, Eme L, Tamarit D, Jørgensen SL, Spang A, Ettema TJG. Chlamydial contribution to mosaic anaerobic metabolism in eukaryotes.
Science Advances 6 (35), eabb7258
[37] Dharamshi JE, Tamarit D*, Eme L*, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG. Marine sediments illuminate Chlamydiae diversity and evolution.
Current Biology. 2020 Mar 5.
2019
[36] Eme L, Ettema TJG. PhyloMagnet: Fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics.
Bioinformatics, btz799.
[35] Karnkowska A, Treitli SC, Brzoň O, Novák L, Vacek V, Soukal P, Barlow LD, Herman EK, Pipaliya SV, Pánek T, Žihala D, Petrželková R, Butenko A, Eme L, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Hampl V. The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion.
Molecular Biology and Evolution, msz147
[34] Muñoz-Gómez SA, Durnin K, Eme L, Paight C, Lane CE, Saffo MB, Slamovits CH. Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts.
Genome Biology and Evolution
[33] Hess S, Eme L, Roger AJ, and Simpson AGB. A natural toroidal microswimmer with a rotary eukaryotic flagellum.
Nature microbiology (2019): 1.
[32] Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, Teske AP, Ettema TJG and Baker BJ. New Asgard archaea capable of anaerobic hydrocarbon cycling.
Nature Communications, 10.
[31] Spang A, Stairs CW, Dombrowski N, Eme L, Lombard J, Fernández-Cáceres E, Greening C, Baker BJ and Ettema TJG. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analysis of Asgard archaeal metabolism.
Nature Microbiology (2019): 1.
2018
[30] Lax G*, Eglit Y*, Eme L*, Bertrand E, Roger AJ, Simpson AGB. Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes.
Nature (2018). doi:10.1038/s41586-018-0708-8
*These authors equally contributed to the manuscript.
[29] Cenci U, Sibbald SJ, Curtis BA, Kamikawa R, Eme L, Moog D, Henrissat B, Marechal E, Chabi M, Djemiel C, Roger AJ, Kim E, Archibald J. Nuclear genome sequence of the plastid- lacking cryptomonad Goniomonas avonlea: phylogenomic and metabolic insights into the evolution of secondary plastids.
BMC Biology. 2018 Dec;16(1):137.
[28] Eme L, Ettema TJG. The eukaryotic ancestor shapes up.
Nature (2018). doi: 10.1038/d41586-018-06868-2
[27] Stairs CW, Eme L, Cohen AM, Dellaire G, Shepherd JN, Fawcett JP, Roger AJ. Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.
eLife 7 (2018): e34292.
[26] Spang A*, Eme L*, Saw J, Caceres EF, Zaremba-Niedzwiedzka K, Lombard J, Guy L, Ettema TJG. Asgard archaea are the closest prokaryotic relatives of eukaryotes. [PDF]
PLoS Genetics 2018, 14(3), e1007080.
*These authors equally contributed to the manuscript.
[25] Leger MM, Eme L, Stairs CW, Roger AJ. Demystifying eukaryote lateral gene transfer. [PDF]
Bioessays 2018 Mar 15:e1700242.
[24] Raina JB, Eme L, Pollock JF, Spang A, Archibald JM, Williams TA. Symbiosis in the microbial world: from ecology to genome evolution. [PDF]
Biology Open .
2017
[23] Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. Archaea and the origin of eukaryotes. [PDF]
Nature Reviews Microbiology 15, 711–723 (2017).
[22] E Gentekaki, BA Curtis, CW Stairs, V Klimeš, M Eliáš, D Salas, EK Herman, L Eme, MC Arias, B Henrissat, F Hilliou, MJ Klute, H Suga, S Malik, AW Pightling, M Kolisko, RA Rachubinski, A Schlacht, DM Soanes, AD Tsaousis, JM Archibald, SG Ball, JB Dacks, CG Clark, M van der Giezen, AJ Roger. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. [PDF]
PLoS biology 15 (9), e2003769.
[21] Eme L, Gentekaki E, Curtis B, Archibald JM, Roger AJ. Lateral gene transfer in the adaption of the anaerobic gut parasite Blastocystis. [PDF]
Current Biology 27 (6), 807-820.
Dispatch: Moreira D., López-García P. Protist Evolution: Stealing Genes to Gut It Out. Current Biology, Volume 27, Issue 6, 20 March 2017, Pages R223-R225.
[20] López-García P, Eme L, D Moreira. Symbiosis in eukaryotic evolution. [PDF]
Journal of Theoretical Biology, 2017.
[19] Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Čepicka I, Silberman JF, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. [PDF]
Nature Ecology & Evolution 1 (2017): 0092.
2016
[18] Eme L, Doolittle WF. Microbial evolution: xenology (apparently) trumps paralogy. [PDF]
Current Biology. 2016 Nov 21;26(22):R1181-3.
[17] Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C, Devos DP. The changing view of eukaryogenesis – fossils, cells, lineages and how they all come together. [PDF]
J Cell Sci. 2016 Oct 15;129(20):3695-703.
[16] Leger MM, Eme L, Hug LA, Roger AJ. Novel mitochondrion-related organelles in the microaerophilic jakobid Stygiella incarcerata. [PDF]
Molecular biology and evolution. 2016 Jun 8:msw103.
[15] Cenci U, Moog D, Curtis BA, Tanifuji G, Eme L, Lukeš J, Archibald JM. Heme pathway evolution in kinetoplastid protists. [PDF]
BMC evolutionary biology. 2016 May 18;16(1):109.
[14] Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P. A eukaryote without a mitochondrial organelle. [PDF]
Current Biology. 2016 May 23;26(10):1274-84.
Media coverage : [ScienceMag] [The Scientist] [PNAS] [Scientific American] [LA Times] [Washington Post] [NPR] [Daily Mail] [CBC] [IFL Science] [Phys.org] [HNGN]
2015
[13] Groussin M, Boussau B, Szöllősi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V. Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. [PDF]
Molecular biology and evolution. 2015 Nov 4:msv249.
[12] Eme L, Doolittle WF. Archaea. [PDF]
Current Biology. 2015 Oct 5;25(19):R851-5.
[11] Eme L, Doolittle WF. Microbial Diversity: A Bonanza of Phyla. [PDF]
Current Biology. 2015 Mar 16;25(6):R227-30.
[10] Torruella G, de Mendoza A, Grau-Bove X, Anto M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. [PDF]
Current Biology. 2015 Sep 21;25(18):2404-10.
[9] Gawryluk RM*, Eme L*, Roger AJ. Gene fusion, fission, lateral transfer, and loss: not-so-rare events in the evolution of eukaryotic ATP citrate lyase. [PDF]
Molecular phylogenetics and evolution. 2015 Oct 31;91:12-6.
*These authors equally contributed to the manuscript.
[8] Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ. An ancestral bacterial division system is widespread in eukaryotic mitochondria. [PDF]
Proceedings of the National Academy of Sciences. 2015 Aug 18;112(33):10239-46.
2014
[7] Eme L, Sharpe SC, Brown MW, Roger AJ.On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. [PDF]
Cold Spring Harbor perspectives in biology. 2014 Aug 1;6(8):a016139.
[6] Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ. A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. [PDF]
Current Biology. 2014 Jun 2;24(11):1176-86.
[5] Tsaousis AD*, Gentekaki E*, Eme L*, Gaston D, Roger AJ. Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes. [PDF]
Eukaryotic cell. 2014 Jan 1;13(1):143-53.
*These authors equally contributed to the manuscript.
2013
[4] Eme L, Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C. Metagenomics of Kamchatkan hot spring filaments reveals two new major (hyper)thermophilic lineages related to Thaumarchaeota. [PDF]
Research in microbiology. 2013 Jun 30;164(5):425-38.
2011
[3] Eme L, Trilles A, Moreira D, Brochier-Armanet C. The phylogenomic analysis of the Anaphase Promoting Complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes. [PDF]
BMC evolutionary biology. 2011 Sep 23;11(1):265.
[2] Boileau C, Eme L, Brochier‐Armanet C, Janicki A, Zhang CC, Latifi A. A eukaryotic-like sulfiredoxin important for peroxiredoxin reduction and oxidative stress response in the cyanobacterium Anabaena PCC 7120. [PDF]
New Phytologist. 2011 Sep 1;191(4):1108-18.
2009
[1] Eme L, Moreira D, Talla E, Brochier-Armanet C. A Complex Cell Division Machinery was Present in the Last Common Ancestor of Eukaryotes. [PDF]
PLoS One. 2009 Apr 7;4(4):e5021.
Book chapters
Dombrowski N, Mahendrarajah T, Gross ST, Eme L, Spang A.
Archaea.
Practical Handbook of Microbiology (p.229-248). 2021/5/4
Sharpe SC*, Eme L*, Brown MW, Roger AJ. Timing the origins of multicellular eukaryotes through phylogenomics and relaxed molecular clock analyses. In Evolutionary Transitions to Multicellular Life 2015 (pp. 3-29). Springer Netherlands.
*These authors equally contributed to the manuscript.
Outreach
Eme L, Ettema TJG. The symbiosis that change the world.
Microbiology today. August 2017.
Oral communications
Invited speaker
2019 Mathematical and Computational Evolutionary Biology conference (Porquerolles, France).
Microbiology Society Conference (Belfast, UK).
EMBO meeting Comparative genomics of Eukaryotic Microbes (San Feliu, Spain).
20e Congres du Groupe Français de Bioénergétique (Autrans, France).
Alphy Comparative Genomics and Bioinformatics (Paris, France).
Gordon Research Seminar (GRC) Archaea (Les diablerets, Switzerland).
2018 Royal Society meeting on the Last Eukaryotic Common Ancestor (Chicheley, UK)
2017 EMBO Comparative Genomics of Microbial Eukaryotes (San Feliu, Spain).
Gordon Research Conference Archaea (Waterville, US).
2016 ASM 2016 – Growing the Tree of Life symposium (Boston, USA).
2015 Company of Biologists Workshop « Eukaryo-/Archaeogenesis: Where Do We Stand? ».
2014 Microbe Evolution 2014 (Tsukuba, Japan).
2009 International Meeting « Archaea and the universal tree of life » (Fondation des Treilles, France).
Selected talks at international conferences
2018 ISEP (International Society of Evolutionary Protistology) (Cyprus). Pinpointing the root of extant eukaryotic diversity.
2017 ICOP (International Congress of Protistology) (Prague, Czech republic). Archaea and the origin of eukaryotes.
2014 ISOP/ISEP meeting 2014 (Banff, Canada). Eme L, Sharpe SC, Brown MW and Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.
2013 ICOP conference (Vancouver, Canada). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut.
SMBE Satellite Eukaryotic-omics (Davis, US). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut.
2012 PROTIST conference (Oslo, Norway). Eme L, Roger AJ. Pinpointing the root of extant eukaryotic diversity
2011 ALPHY meeting (Bioinformatics et evolutionary genomics) (Lyon, France).
Eme L, Moreira D, Brochier-Armanet C. The phylogenomic analysis of the ACP/C and its targets points to a complex and modern-like control of the cell cycle in LECA.
2009 ALPHY meeting (Montpellier, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. A complex cell division machinery in the last common ancestor of eukaryotes
Poster presentations
2015 – ECOP (European Congress of Protistology) (Seville, Spain). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.
2015 – SMBE (Society for Molecular Biology and Evolution) (Vienna, Austria). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.
2010 – SMBE (Society for Molecular Biology and Evolution) (Lyon, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. Tracing back the nature of cell division in the Last Common Ancestor of Eukaryotes.
2009 – EMBO 2009 conference Comparative Genomics of Eukaryotic Microorganisms. (San Feliu de Guixols, Spain). Eme L, Moreira D, Brochier-Armanet C Phylogenomic study of cytokinesis in Eukaryotes
Eukaryotic Cell Journal Outstanding Young Investigator Award.
2009 – Graduate School Meeting (Marseilles, France).
Eme L, Moreira D, Brochier-Armanet C A complex cell division machinery in the last common ancestor of eukaryotes. Best Poster Award.
2007 – JOBIM conference (Marseille, France). Eme L, Moreira D, Brochier-Armanet C Origin and evolution of the eukaryotic midbody: A phylogenomic approach