The macroevolutionary impact of epigenetics and lateral gene transfer on eukaryotic genomes

Project Information

Macro-EpiK

Grant agreement ID: 803151

DOI

10.3030/803151

Project closed

EC signature date 10 October 2018

Start date 1 March 2019

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 945,00

EU contribution

€ 1 499 945,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Open Research Data Pilot (1)

Data Management Plan

Participation to the Open Research Data Pilot

Publications

Peer reviewed articles (20)

Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species

Author(s): Ludek Koreny, Mohammad Zeeshan, Konstantin Barylyuk, Eelco C. Tromer, Jolien J. E. van Hooff, Declan Brady, Huiling Ke, Sara Chelaghma, David J. P. Ferguson, Laura Eme, Rita Tewari, Ross F. Waller
Published in: PLOS Biology, Issue 19/3, 2021, Page(s) e3001081, ISSN 1545-7885
Publisher: PLOS
DOI: 10.1371/journal.pbio.3001081

One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

Author(s): Jazmin Blaz, Luis Javier Galindo, Aaron A. Heiss, Harpreet Kaur, Guifré Torruella, Ashley Yang, L. Alexa Thompson, Alexander Filbert, Sally Warring, Apurva Narechania, Takashi Shiratori, Ken-ichiro Ishida, Joel B. Dacks, Purificación López-García, David Moreira, Eunsoo Kim, Laura Eme
Published in: Scientific Data, Issue 10, 2023, ISSN 2052-4463
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41597-023-02488-2

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

Author(s): Lukáš V. F. Novák, Sebastian C. Treitli, Jan Pyrih, Paweł Hałakuc, Shweta V. Pipaliya, Vojtěch Vacek, Ondřej Brzoň, Petr Soukal, Laura Eme, Joel B. Dacks, Anna Karnkowska, Marek Eliáš, Vladimír Hampl
Published in: PLOS Genetics, Issue 19, 2023, Page(s) e1011050, ISSN 1553-7404
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pgen.1011050

Releasing uncurated datasets is essential for reproducible phylogenomics

Author(s): Eric D. Salomaki, Laura Eme, Matthew W. Brown, Martin Kolisko
Published in: Nature Ecology & Evolution, Issue 4/11, 2020, Page(s) 1435-1437, ISSN 2397-334X
Publisher: Nature Publishing Group
DOI: 10.1038/s41559-020-01296-w

A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses

Author(s): Daniel Tamarit, Eva F. Caceres, Mart Krupovic, Reindert Nijland, Laura Eme, Nicholas P. Robinson, Thijs J. G. Ettema
Published in: Nature Microbiology, Issue 7, 2022, Page(s) 948-952, ISSN 2058-5276
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41564-022-01122-y

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

Author(s): Jennah E. Dharamshi, Daniel Tamarit, Laura Eme, Courtney W. Stairs, Joran Martijn, Felix Homa, Steffen L. Jørgensen, Anja Spang, Thijs J.G. Ettema
Published in: Current Biology, Issue 30/6, 2020, Page(s) 1032-1048.e7, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2020.02.016

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing-Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Published in: PLOS Biology, Issue 19/8, 2021, Page(s) e3001365, ISSN 1545-7885
Publisher: PLOS
DOI: 10.1371/journal.pbio.3001365

Reconstructing the last common ancestor of all eukaryotes

Author(s): Thomas A. Richards, Laura Eme, John M. Archibald, Guy Leonard, Susana M. Coelho, Alex de Mendoza, Christophe Dessimoz, Pavel Dolezal, Lillian K. Fritz-Laylin, Toni Gabaldón, Vladimír Hampl, Geert J. P. L. Kops, Michelle M. Leger, Purificacion Lopez-Garcia, James O. McInerney, David Moreira, Sergio A. Muñoz-Gómez, Daniel J. Richter, Iñaki Ruiz-Trillo, Alyson E. Santoro, Arnau Sebé-Pedrós, Be
Published in: PLOS Biology, Issue 22, 2024, Page(s) e3002917, ISSN 1545-7885
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pbio.3002917

Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes

Author(s): Shannon J. Sibbald, Laura Eme, John M. Archibald, Andrew J. Roger
Published in: Trends in Parasitology, Issue 36/11, 2020, Page(s) 927-941, ISSN 1471-4922
Publisher: Elsevier BV
DOI: 10.1016/j.pt.2020.07.014

Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes

Author(s): Courtney W. Stairs, Petr Táborský, Eric D. Salomaki, Martin Kolisko, Tomáš Pánek, Laura Eme, Miluše Hradilová, Čestmír Vlček, Jon Jerlström-Hultqvist, Andrew J. Roger, Ivan Čepička
Published in: Current Biology, 2021, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2021.10.010

Chlamydial contribution to anaerobic metabolism during eukaryotic evolution

Author(s): Courtney W. Stairs, Jennah E. Dharamshi, Daniel Tamarit, Laura Eme, Steffen L. Jørgensen, Anja Spang, Thijs J. G. Ettema
Published in: Science Advances, Issue 6/35, 2020, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abb7258

Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria

Author(s): Sergio A. Muñoz-Gómez, Edward Susko, Kelsey Williamson, Laura Eme, Claudio H. Slamovits, David Moreira, Purificación López-García, Andrew J. Roger
Published in: Nature Ecology & Evolution, Issue 6, 2022, Page(s) 253-262, ISSN 2397-334X
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41559-021-01638-2

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution

Author(s): Tom A Williams, Adrian A Davin, Lénárd L Szánthó, Alexandros Stamatakis, Noah A Wahl, Ben J Woodcroft, Rochelle M Soo, Laura Eme, Paul O Sheridan, Cecile Gubry-Rangin, Anja Spang, Philip Hugenholtz, Gergely J Szöllősi
Published in: The ISME Journal, Issue 18, 2024, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1093/ismejo/wrae129

A gene-rich mitochondrion with a unique ancestral protein transport system

Author(s): David Moreira, Jazmin Blaz, Eunsoo Kim, Laura Eme
Published in: Current Biology, Issue 34, 2025, Page(s) 3812-3819.e3, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2024.07.017

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Author(s): Laura Eme, Daniel Tamarit, Eva F. Caceres, Courtney W. Stairs, Valerie De Anda, Max E. Schön, Kiley W. Seitz, Nina Dombrowski, William H. Lewis, Felix Homa, Jimmy H. Saw, Jonathan Lombard, Takuro Nunoura, Wen-Jun Li, Zheng-Shuang Hua, Lin-Xing Chen, Jillian F. Banfield, Emily St John, Anna-Louise Reysenbach, Matthew B. Stott, Andreas Schramm, Kasper U. Kjeldsen, Andreas P. Teske, Brett J. Baker,
Published in: Nature, Issue 618, 2024, Page(s) 992-999, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-06186-2

Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher

Author(s): Robert E. Jones, Alexander K. Tice, Marek Eliáš, Laura Eme, Martin Kolísko, Serafim Nenarokov, Tomáš Pánek, Antonis Rokas, Eric Salomaki, Jürgen F. H. Strassert, Xing‐Xing Shen, David Žihala, Matthew W. Brown
Published in: Current Protocols, Issue 4, 2024, ISSN 2691-1299
Publisher: Wiley
DOI: 10.1002/cpz1.969

Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments

Author(s): Brittany A. Baker, Ana Gutiérrez-Preciado, Álvaro Rodríguez del Río, Charley G. P. McCarthy, Purificación López-García, Jaime Huerta-Cepas, Edward Susko, Andrew J. Roger, Laura Eme, David Moreira
Published in: Nature Microbiology, Issue 9, 2024, Page(s) 964-975, ISSN 2058-5276
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41564-024-01647-4

Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida

Author(s): Naoji Yubuki, Guifré Torruella, Luis Javier Galindo, Aaron A. Heiss, Maria Cristina Ciobanu, Takashi Shiratori, Ken‐ichiro Ishida, Jazmin Blaz, Eunsoo Kim, David Moreira, Purificación López‐García, Laura Eme
Published in: Journal of Eukaryotic Microbiology, Issue 70, 2023, ISSN 1066-5234
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/jeu.12997

GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models

Author(s): Hector Banos, Thomas K F Wong, Justin Daneau, Edward Susko, Bui Quang Minh, Robert Lanfear, Matthew W Brown, Laura Eme, Andrew J Roger
Published in: Molecular Biology and Evolution, Issue 41, 2024, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msae174

Independent Size Expansions and Intron Proliferation in Red Algal Plastid and Mitochondrial Genomes

Author(s): Fabian van Beveren, Laura Eme, Purificación López-García, Maria Ciobanu, David Moreira
Published in: Genome Biology and Evolution, Issue 14, 2022, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evac037

Non-peer reviewed articles (2)

Microbial Diversity and Open Questions about the Deep Tree of Life

Author(s): Laura Eme, Daniel Tamarit
Published in: Genome Biology and Evolution, Issue 16, 2024, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evae053

Life through the lens of metabolism

Author(s): Laura Eme, Courtney W. Stairs
Published in: Nature Ecology & Evolution, Issue 6, 2022, Page(s) 1590-1590, ISSN 2397-334X
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41559-022-01880-2