2024
Rubén González-Miguéns, Alex Gàlvez-Morante, Margarita Skamnelou, Meritxell Antó, Elena Casacuberta, Daniel J. Richter, Daniel Vaulot, Javier del Campo, Iñaki Ruiz-Trillo (2024)
A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses.
Preprint available at Research Square
Marta Álvarez-Presas, Iñaki Ruiz-Trillo, Jordi Paps (2024)
Novel genomic approaches support Xenacoelomorpha as sister to all Bilateria.
bioRxiv 2024.12.05.626972
Thomas A. Richards, Laura Eme, John M. Archibald, [...], Michelle M. Leger, [...], Iñaki Ruiz-Trillo, [...], Jeremy G. Wideman (2024)
Reconstructing the last common ancestor of all eukaryotes.
PLOS Biology 22(11): e3002917
Victoria Shabardina, Jennah E. Dharamshi, Patricia S. Ara, Meritxell Antó, Fernando J. Bascón, Hiroshi Suga, Wyth Marshall, Claudio Scazzocchio, Elena Casacuberta & Iñaki Ruiz-Trillo (2024)
Ichthyosporea: a window into the origin of animals.
Communications Biology | (2024)7:915
Benvenuto G, Leone S, Astoricchio E, Bormke S, Jasek S, D'Aniello E, Kittelmann M, McDonald K, Hartenstein V, Baena V, Escrivà H, Bertrand S, Schierwater B, Burkhardt P, Ruiz-Trillo I, Jékely G, Ullrich-Lüter J, Lüter C, D'Aniello S, Arnone MI, Ferraro F. (2024)
Evolution of the ribbon-like organization of the Golgi apparatus in animal cells.
Cell Rep. 2024 Feb 26:113791
2023
Iñaki Ruiz-Trillo, Koryu Kin, Elena Casacuberta (2023)
The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event.
Annual Review of Microbiology 77:499-516
Steven Boeynaems, Yanniv Dorone, Yanrong Zhuang, Victoria Shabardina, Guozhong Huang, Anca Marian, Garam Kim, Anushka Sanyal, Nesli-Ece Şen, Daniel Griffith, Roberto Docampo, Keren Lasker, Iñaki Ruiz-Trillo, Georg Auburger, Alex S. Holehouse, Edor Kabashi, Yi Lin, Aaron D. Gitler (2023)
Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates.
Molecular Cell 83, 1–15
Núria Ros-Rocher, Ria Q. Kidner , Catherine Gerdt, W. Sean Davidson , Iñaki Ruiz-Trillo and Joseph P. Gerdt (2023)
Chemical factors induce aggregative multicellularity in a close unicellular relative of animals.
PNAS 110 (18): e2216668120
Sergio A. Muñoz-Gómez, Lawrence Rudy Cadena, Alastair T. Gardiner, Michelle M. Leger, Shaghayegh Sheikh, Louise B. Connell, Tomáš Bilý, Karel Kopejtka, J. Thomas Beatty, Michal Koblížek, Andrew J. Roger, Claudio H. Slamovits, Julius Lukeš, Hassan Hashimi (2023)
Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60.
Current Biology 33, 1–13
Konstantina Mitsi, Daniel J. Richter, Alicia S. Arroyo, David López-Escardó, Meritxell Antó, Antonio Guillén Oterino and Iñaki Ruiz-Trillo (2023)
Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding.
Sci Rep 13, 3119 (2023)
Pei Zhang, Yuanzhen Zhu, Qunfei Guo, Ji Li, Xiaoyu Zhan, Hao Yu, Nianxia Xie, Huishuang Tan, Nina Lundholm, Lydia Garcia-Cuetos, Michael D. Martin, Meritxell Antó Subirats, Yi-Hsien Su, Iñaki Ruiz-Trillo, Mark Q. Martindale, Jr-Kai Yu, M. Thomas P. Gilbert, Guojie Zhang and Qiye Li (2023)
On the origin and evolution of RNA editing in metazoans.
Cell Reports 42 (2), 112112
Victoria Shabardina, Pedro Romero Charria, Gonzalo Bercedo Saborido, Ester Diaz-Mora, Ana Cuenda, Iñaki Ruiz-Trillo & Juan Jose Sanz-Ezquerro (2023)
Evolutionary analysis of p38 stress-activated kinases in unicellular relatives of animals suggests an ancestral function in osmotic stress.
Open Biol.13: 220314.
2022
Eduard Ocaña-Pallarès, Tom A. Williams, David López-Escardó, Alicia S. Arroyo, Jananan S. Pathmanathan, Eric Bapteste, Denis V. Tikhonenkov, Patrick J. Keeling, Gergely J. Szöllősi & Iñaki Ruiz-Trillo (2022)
Divergent genomic trajectories predate the origin of animals and fungi.
Nature 609, 747–753 (2022)
Xavier Grau-Bové, Cristina Navarrete, Cristina Chiva, Thomas Pribasnig, Meritxell Antó, Guifré Torruella, Luis Javier Galindo, Bernd Franz Lang, David Moreira, Purificación López-Garcia, Iñaki Ruiz-Trillo, Christa Schleper, Eduard Sabidó & Arnau Sebé-Pedrós (2022)
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.
Nature Ecology and Evolution 6, 1007–1023 (2022)
Omaya Dudin, Sébastien Wielgoss, Aaron M. New, Iñaki Ruiz-Trillo (2022)
Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals.
PLoS Biol 20(3): e3001551
Aleksandra Kozyczkowska, Iñaki Ruiz-Trillo, Elena Casacuberta (2022)
Unicellular Relatives of Animals.
In “Handbook of Marine Model Organisms in Experimental Biology. Established and emerging”. Agnès Boutet, Bernd Schierwater.
CRC Press
Michelle M. Leger, Núria Ros-Rocher, Sebastian R. Najle, Iñaki Ruiz-Trillo (2022)
Rel/NF-κB transcription factors emerged at the onset of opisthokonts.
Genome Biology and Evolution, evab289
2021
Iva Guberovic, Sarah Hurtado-Bagès, Ciro Rivera-Casas, Gunnar Knobloch, Roberto Malinverni1, Vanesa Valero, Michelle M. Leger, Jesús García, Jerome Basquin, Marta Gómez de Cedrón, Marta Frigolé-Vivas, Manjinder S. Cheema, Ainhoa Pérez, Juan Ausió9 , Ana Ramírez de Molina8, Xavier Salvatella, Iñaki Ruiz-Trillo, Jose M. Eirin-Lopez , Andreas G. Ladurner and Marcus Buschbeck (2021)
Evolution of a histone variant involved in compartmental regulation of NAD metabolism.
Nature Structural & Molecular Biology 28, pages1009–1019 (2021)
Michelle M. Leger & Iñaki Ruiz-Trillo (2021)
Phylogenetics of clonal multicellularity.
In "The Evolution of Multicellularity". Mathew D. Herron, Peter L. Conlin, William C. Ratcliff.
CRC Press
Nicolas Rosa, Hristina Ivanona, Larry E. Wagner 2nd, Justin Kale, Rita La Rovere, Kirsten Welkenhuyzen, Nikolaos Louros, Spyridoula Karamanou, Victoria Shabardina, Irma Lemmens, Elien Vandermarliere, Kozo Hamada, Hideaki Ando, Frederic Rousseau, Joost Schymkowitz, Jan Tavernier, Katsuhiko Mikoshiba, Anastassios Economou, David W Andrews, Jan B Parys, David I Yule, Geert Bultynck (2021)
Bcl-xL acts as an inhibitor of IP 3 R channels, thereby antagonizing Ca 2+-driven apoptosis.
Cell Death Differ. 2021 Nov 8. doi: 10.1038/s41418-021-00894-w
Ander Urrutia, Konstantina Mitsi, Rachel Foster, Stuart Ross, Martin Carr, Georgia M. Ward, Ronny van Aerle, Ionan Marigomez, Michelle M. Leger, Iñaki Ruiz-Trillo, Stephen W. Feist, David Bass (2021)
Txikispora philomaios n. sp., n. g., a Micro-Eukaryotic Pathogen of Amphipods, Reveals Parasitism and Hidden Diversity in Class Filasterea.
Journal of Eukarytioc Microbiology doi:10.1111/jeu.12875
Nicolas Rosa, Victoria Shabardina, Hristina Ivanova, Arnau Sebé-Pedrós, David I.Yulec, Geert Bultyncka (2021)
Tracing the evolutionary history of Ca2+-signaling modulation by human Bcl-2: Insights from the Capsaspora owczarzaki IP3 receptor ortholog.
BBA-Molecular Cell Research 1868(12):119121
Michelle M. Leger & Iñaki Ruiz-Trillo (2021)
The Closest Unicellular Relative of Animals.
In "Invertebrate Zoology. A Tree of Life Approach" . Bernd Schierwater, Rob DeSalle.
CRC Press. https://doi.org/10.1201/9780429159053
Aleksandra Kozyczkowska, Sebastian R. Najle, Eduard Ocaña-Pallarés, Cristina Aresté, Victoria Shabardina, Patricia S. Ara, Iñaki Ruiz-Trillo, Elena Casacuberta (2021)
Stable transfection in protist Corallochytrium limacisporum identifies novel cellular features among unicellular animals relatives.
Current Biology 31, 4104-4110
Sebastián R. Najle & Iñaki Ruiz-Trillo (2021)
The Protistan Origins of Animal Cell Differentiation.
In "Origin and Evolution of Metazoan Cell" Leys & Hejnol
CRC Press; Evolutionary Cell Biology Series
Núria Ros-Rocher, Alberto Pérez-Posada, Michelle M. Leger and Iñaki Ruiz-Trillo (2021)
The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition.
Open Biol. 11: 200359. https://doi.org/10.1098/rsob.200359
2020
Iñaki Ruiz-Trillo & Alex de Mendoza (2020)
Towards understanding the origin of animal development.
Development 2020 147(23): dev192575
Helena Parra-Acero, Matija Harcet, Núria Sánchez-Pons, Elena Casacuberta, Nicholas H Brown, Omaya Dudin, and Iñaki Ruiz-Trillo (2020)
Integrin-Mediated Adhesion in the Unicellular Holozoan Capsaspora owczarzaki.
Current Biology 30, 1-6
Yameng Lu, Eduard Ocaña-Pallarès, David López-Escardó, Stuart R Dennis, Michael T Monaghan, Iñaki Ruiz-Trillo, Piet Spaak, Justyna Wolinska (2020)
Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes.
Molecular phylogenetics and evolution 151 (2020) 106891
Alicia S. Arroyo, Roman Iannes, Eric Bapteste, Iñaki Ruiz-Trillo (2020)
Gene similarity networks unveil a potential novel unicellular group closely related to animals from the Tara Oceans expedition.
Genome Biology and Evolution 12 (9): 1664-1678
Anderson da Silva, Hélio Nobre Jr, Leticia Sampaio, Bruna do Nascimento, Cecilia da Silva, João Batista de Andrade Neto, Ángeles Manresa, Aurora Pinazo, Bruno Cavalcanti, Manoel Odorico de Moraes, Iñaki Ruiz-Trillo, Meritxell Antó, Carmen Morán, Lourdes Pérez (2020)
Antifungal and antiprotozoal green amino acid-based rhamnolipids: Mode of action, antibiofilm efficiency and selective activity against resistant Candida spp. strains and Acanthamoeba castellanii.
Colloids and Surfaces B: Biointerfaces, 193:111148
Eduard Ocaña-Pallarès, Zaida Vergara, Bénédicte Desvoyes, Manuel Tejada-Jimenez, Ainoa Romero-Jurado, Aurora Galván, Emilio Fernández, Iñaki Ruiz-Trillo, Crisanto Gutierrez (2020)
Origin recognition complex (ORC) evolution is influenced by global gene duplication/loss patterns in eukaryotic genomes.
Genome biology and evolution 12 (2): 3878-3889
D Faktorová, RER Nisbet, JAF Robledo, E Casacuberta, L Sudek, …Iñaki Ruiz-Trillo et al (2020)
Genetic tool development in marine protists: Emerging model organisms for experimental cell biology.
Nature methods 17 (5), 481-494
Alberto Pérez-Posada, Omaya Dudin, Eduard Ocaña-Pallarès, Iñaki Ruiz- Trillo, Andrej Ondracka (2020)
Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery.
Plos Genetics 16 (3), e1008584
2019
Daniel J Richter, Tera C Levin (2019)
The origin and evolution of cell-intrinsic antibacterial defenses in eukaryotes.
Current Opinion in Genetics and Development (2019) 59:111-122
Omaya Dudin, Andrej Ondracka, Xavier Grau-Bové, Arthur AB Haraldsen, Atsushi Toyoda, Hiroshi Suga, Jon Bråte, Iñaki Ruiz-Trillo (2019)
A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization.
eLife 2019;8:e49801
David López-Escardó, Xavier Grau-Bové, Amy Guillaumet-Adkins, Marta Gut, Michael E. Sieracki, Iñaki Ruiz-Trillo (2019)
Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.
Philosophical Transactions of the Royal Society B 374: 20190088
Konstantina Mitsi, Alicia S. Arroyo, Iñaki Ruiz-Trillo (2019)
A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.
Biology Letters 15: 20190182
Seitaro Denbo, Katsutoshi Aono, Takaaki Kai, Rei Yagasaki, Iñaki Ruiz-Trillo, Hiroshi Suga (2019)
Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome.
Development Growth & Differentation 61(1): 34–42
Eduard Ocaña-Pallarès, Sebastián R. Najle, Claudio Scazzocchio, Iñaki Ruiz-Trillo (2019)
Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway.
PLoS GENETICS15(2): e1007986
Maureen A. O’Malley, Michelle M. Leger, Jeremy G. Wideman and Iñaki Ruiz-Trillo (2019)
Concepts of the last eukaryotic common ancestor.
Nature Ecology & Evolution 3, 338–344
2018
Àlbert Rafels-Ybern, Adrian Gabriel Torres, Noelia Camacho, Andrea Herencia-Ropero, Helena Roura Frigolé, Thomas F Wulff, Marina Raboteg, Albert Bordons, Xavier Grau-Bové, Iñaki Ruiz-Trillo, Lluís Ribas de Pouplana (2018)
The expansion of Inosine at the wobble position of tRNAs, and its role in the evolution of proteomes.
Molecular Biology and Evolution 36(4):650–662
Iñaki Ruiz-Trillo y Maria Ferrer-Bonet (2018)
¿Con quién compartimos el planeta?
Investigación y Ciencia. Diciembre 2018
Jon Brate, Ralf S. Neumann, Bastian Fromm, Arthur A.B. Haraldsen, James E. Tarver, Hiroshi Suga, Philip C.J. Donoghue, Kevin J. Peterson, Iñaki Ruiz-Trillo, Paul E. Grini, and Kamran Shalchian-Tabrizi (2018)
Unicellular Origin of the Animal MicroRNA Machinery.
Current Biology 28(20):3288-3295.e5
Sina M. Adl, David Bass, Christopher E. Lane, Julius Lukeš, Conrad L. Schoch, Alexey Smirnov, Sabine Agatha, Cedric Berney, Matthew W. Brown, Fabien Burki, Paco Cárdenas, Ivan Čepička, Ludmila Chistyakova, Javier del Campo, Micah Dunthorn, Bente Edvardsen, Yana Eglit, Laure Guillou, Vladimír Hampl, Aaron A. Heiss, Mona Hoppenrath, Timothy Y. James, Sergey Karpov, Eunsoo Kim, Martin Kolisko, Alexander Kudryavtsev, Daniel J. G. Lahr, Enrique Lara, Line Le Gall, Denis H. Lynn, David G. Mann, Ramon Massana i Molera, Edward A. D. Mitchell, Christine Morrow, Jong Soo Park, Jan W. Pawlowski, Martha J. Powell, Daniel J. Richter, Sonja Rueckert, Lora Shadwick, Satoshi Shimano, Frederick W. Spiegel, Guifré Torruella i Cortes, Noha Youssef, Vasily Zlatogursky, Qianqian Zhang (2018)
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.
Journal of Eukaryotic Microbiology 2019, 66, 4-119
Xavier Grau-Bové, Iñaki Ruiz-Trillo and Manuel Irimia (2018).
Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture.
Genome Biology 19,135 (2018)
David López-Escardó, Jordi Paps, Colomban de Vargas, Ramon Massana, Iñaki Ruiz-Trillo & Javier del Campo (2018)
Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity.
Scientific Reports 8, 9106 (2018)
Alicia S. Arroyo, David López-Escardó, Eunsoo Kim, Iñaki Ruiz-Trillo, and Sebastián R. Najle (2018)
Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans revealed by Metabarcoding in Middle Paraná River, Argentina.
Frontiers in Ecology and Evolution 6:99
Vidyanand Nanjundiah, Iñaki Ruiz-Trillo, and David Kirk (2018)
Protists and Multiple Routes to the Evolution of Multicellularity.
In “Cells in Evolutionary Biology: Translating Genotypes into Phenotypes – Past, Present, Future”. Brian K. Hall, Sally A. Moody eds.
CRC Press; Evolutionary Cell Biology Series
Andrej Ondracka, Omaya Dudin & Iñaki Ruiz-Trillo (2018)
Decoupling of Nuclear Division Cycles and Cell Size during the Coenocytic Growth of the Ichthyosporean Sphaeroforma arctica.
Current Biology 28(12), 1964-1969.e2
Michelle M. Leger, Laura Eme, Courtney W. Stairs, Andrew J. Roger (2018)
Demystifying Eukaryote Lateral Gene Transfer.
BioEssays 2018 40, 1700242
Guy Leonard, Aurélie Labarre, David S. Milner, Adam Monier, Darren Soanes, Jeremy G. Wideman, Finlay Maguire, Sam Stevens, Divya Sain, Xavier Grau-Bové, Arnau Sebé-Pedrós, Jason E. Stajich, Konrad Paszkiewicz, Matthew W. Brown, Neil Hall, Bill Wickstead, Thomas A. Richards (2018)
Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides
Open Biology 8: 170184
Helena Parra-Acero, Núria Ros-Rocher, Alberto Perez-Posada, Aleksandra Kożyczkowska, Núria Sánchez-Pons, Azusa Nakata, Hiroshi Suga, Sebastián R. Najle, Iñaki Ruiz-Trillo (2018)
Transfection of Capsaspora owczarzaki, a close unicellular relative of animals.
Development 145 (10): dev162107
Helena Ćetković, Maja Herak Bosnar, Drago Perina, Andreja Mikoč, Martina Deželjin, Robert Beluži, Helena Bilandžija, Iñaki Ruiz-Trillo & Matija Harcet (2018)
Characterization of a group I Nme protein of Capsaspora owczarzaki—a close unicellular relative of animals.
Laboratory Investigation 98, 304-314 (2018)
2017
Albert Rafels-Ybern, Adrian Gabriel Torres, Xavier Grau-Bové, Iñaki Ruiz-Trillo & Lluís Ribas de Pouplana (2017)
Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla.
RNA Biology 15:4-5, 500-507
David López-Escardó, Xavier Grau-Bové, Amy Gillaumet-Adkins, Marta Gut, Michael E. Sieracki & Iñaki Ruiz-Trillo (2017)
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.
Scientific Reports 7,11025 (2017)
Maria Ferrer-Bonet & Iñaki Ruiz-Trillo (2017)
Capsaspora owczarzaki.
Current Biology 27(17), PR829-R830
Xavier Grau-Bové, Guifré Torruella, Stuart Donachie, Hiroshi Suga, Guy Leonard, Thomas A. Richards & Iñaki Ruiz-Trillo (2017)
Dynamics of genomic innovation in the unicellular ancestry of animals.
eLife 2017;6:e26036
David López-Escardó, Purificación López-García, David Moreira, Iñaki Ruiz-Trillo & Guifré Torruella (2017)
Parvularia atlantis gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta).
Journal of Eukaryotic Microbiology 2018 65, 170-179
Arnau Sebé-Pedrós, Bernard M. Degnan & Iñaki Ruiz-Trillo (2017)
The origin of Metazoa: a unicellular perspective.
Nature Review Genetics 18, 498–512 (2017)
2016
Arnau Sebé-Pedrós, Marcia Ivonne Peña, Salvador Capella-Gutiérrez, Meritxell Antó, Toni Gabaldón, Iñaki Ruiz-Trillo & Eduard Sabidó (2016)
High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.
Developmental Cell 39 (2): p186–197
Watch video abstract:
Alicia S. Arroyo, David López-Escardó, Colomban de Vargas & Iñaki Ruiz-Trillo (2016)
Hidden diversity of Acoelomorpha revealed through metabarcoding.
Biology Letters 12: 20160674
Access supplementary material
Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo (2016)
Evolution and Classification of the T-Box Transcription Factor Family.
Current Topics in Developmental Biology, 122: p1-26
Maureen A. O’Malley, Jeremy G. Wideman & Iñaki Ruiz-Trillo (2016)
Losing complexity: the role of simplification in macroevolution.
Trends in Ecology and Evolution 31(8):608-621
Sebastián R. Najle, María Celeste Molina, Iñaki Ruiz-Trillo & Antonio D. Uttaro (2016)
Sterol metabolism in the filasterean Capsaspora owczarzaki has features that resemble both fungi and animals.
Open Biology 6: 160029
Arnau Sebé-Pedrós, Cecillia Ballaré, Helena Parra-Acero, Cristina Chiva, Juan J. Tena, Eduard Sabidó, José Luis Gómez-Skarmeta, Luciano Di Croce, Iñaki Ruiz-Trillo (2016)
The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity.
Cell 165 (5): 1224–1237
See Nature’s news and views or watch video abstract:
Mariona Esquerdo, Xavier Grau-Bové, Alejandro Garanto, Vasileios Toulis, Sílvia Garcia-Monclús, Erica Millo, Mª José López-Iniesta, Víctor Abad-Morales, Iñaki Ruiz-Trillo, Gemma Marfany (2016)
Expression atlas of the deubiquitinating enzymes in the adult mouse retina, their evolutionary diversification and phenotypic roles.
PLoS ONE 11(3): e0150364
David A. Gold, Jonathan Grabenstatter, Alex de Mendoza, Ana Riesgo, Iñaki Ruiz-Trillo and Roger E. Summons (2016)
Sterol and genomic analyses validate the sponge biomarker hypothesis.
PNAS 113(10): 2684-2689
Iñaki Ruiz-Trillo (2016)
What are the genomes of the premetazoan lineages telling us about the origins of metazoa?
Multicellularity: Origins and Evolution
Iñaki Ruiz-Trillo & Jordi Paps (2016)
Acoelomorpha: earliest-branching bilaterians or deuterostomes?
Organisms Diversity and Evolution (2016) 16: 391-399
2015
Alex de Mendoza, Hiroshi Suga, Jon Permanyer, Manuel Irimia, Iñaki Ruiz-Trillo (2015)
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.
eLife 2015; 4:e08904
Access Creolimax fragrantissima’s genome
Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, Mark A. Chaplin, Javier del Campo, Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie, and Iñaki Ruiz-Trillo (2015)
Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.
Current Biology 25(18):2404-10
Xavier Grau-Bové, Iñaki Ruiz-Trillo, & Francisco Rodriguez-Pascual (2015)
Origin and evolution of lysyl oxidases.
Scientific Reports 5:10568
Kamil J. Alzayady, Arnau Sebé-Pedrós, Rahul Chandrasekhar, Liwei Wang, Iñaki Ruiz- Trillo, David I. Yule (2015)
Tracing the Evolutionary History of Inositol, 1, 4, 5-trisphosphate receptor: Insights from Analyses of Capsaspora owczarzaki Ca2+ Release Channel Orthologs.
Molecular Biology and Evolution 32 (9): 2236-2253
Iñaki Ruiz-Trillo & Aurora Nedelcu (editors) (2015)
Evolutionary transitions to multicellular life: principles and mechanisms.
Advances in Marine Genomics Series. Springer.
Hiroshi Suga and Iñaki Ruiz-Trillo (2015)
Unraveling the origin of animal multicellularity.
Jikken Igaku (Experimental Medicine) vol.33, no.6, pp968-973.
Javier del Campo, Diego Mallo, Ramon Massana, Colomban de Vargas, Tom A. Richards & Iñaki Ruiz-Trillo (2015)
Diversity and distribution of unicellular opisthokonts along the European coast analyzed using high-throughput sequencing.
Environmental Microbiology (2015)17(9), 3195–3207
2014
Xavier Grau-Bové, Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo (2014)
The eukaryotic ancestor had a complex ubiquitin signalling system of archaeal origin.
Molecular Biology and Evolution 32 (3): 726-739
Alex de Mendoza & Iñaki Ruiz-Trillo (2014)
Multicellularity: Forward genetics for back-in-time questions.
eLife 2014 3:e05218
Javier del Campo, Michael E. Sieracki, Robert Molestina, Patrick Keeling, Ramon Massana & Iñaki Ruiz-Trillo (2014)
The others: our biased perspective of eukaryotic genomics.
Trends in Ecology and Evolution 29(5): 252-259
Alex de Mendoza, Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo (2014)
The evolution of the GPCR signalling system in eukaryotes: modularity, conservation and the transition to metazoan multicellularity.
Genome Biology and Evolution 6(3):606-19
Arnau Sebé-Pedrós, Xavier Grau-Bové, Thomas A. Richards & Iñaki Ruiz-Trillo (2014)
Evolution and classification of myosins, a paneukaryotic whole genome approach.
Genome Biology and Evolution 6(2):290-305
Access myosins dataset
Hiroshi Suga, Guifré Torruella, Gertraud Burger, Matthew W. Brown & Iñaki Ruiz-Trillo (2014)
Earliest holozoan expansion of phosphotyrosine signaling.
Molecular Biology and Evolution 31 (3): 517-528
Bénédicte Desvoyes, Alex de Mendoza, Iñaki Ruiz-Trillo and Crisanto Gutierrez (2014)
Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division.
Journal of Experimental Botany 65(10): 2654-66
2013
Arnau Sebé-Pedrós, Manuel Irimia, Javier del Campo, Helena Parra-Acero, Carsten Russ, Chad Nusbaum, Benjamin J. Blencowe & Iñaki Ruiz-Trillo (2013)
Regulated aggregative multicellularity in a close unicellular relative of Metazoa.
eLife 2013;2:e01287
Access RNAseq data (FPKMs).
Alex de Mendoza, Arnau Sebé-Pedrós, Martin Sebastijan Šestak, Marija Matejčić, Guifré Torruella, Tomislav Domazet-Lošo & Iñaki Ruiz-Trillo (2013)
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages.
Proceedings National Academic of Sciences USA 110 (50) E4858-E4866
Arnau Sebé-Pedrós, Ana Ariza-Cosano, Matthew T. Weirauch, Sven Leininger, Ally Yang, Guifré Torruella, Marcin Adamski, Maja Adamska, Timothy R. Hughes, José Luis Gómez-Skarmeta & Iñaki Ruiz-Trillo (2013)
Early evolution of the T-box transcription factor family.
Proceedings National Academic of Sciences USA 110(40):16050-16055
Arnau Sebé-Pedrós, Pawel Burkhardt, Núria Sánchez-Pons, Stephen R. Fairclough, B. Franz Lang, Nicole King & Iñaki Ruiz-Trillo (2013)
Insights into the origin of metazoan filopodia and microvilli.
Molecular Biology and Evolution 30(9):2013-2023
Hiroshi Suga, Zehua Chen, Alex de Mendoza, Arnau Sebé-Pedrós, Matthew W. Brown, Eric Kramer, Martin Carr, Pierre Kerner, Michel Vervoort, Núria Sánchez-Pons, Guifré Torruella, Romain Derelle, Gerard Manning, B. Franz. Lang, Carsten Russ, Brian J. Haas, Andrew J. Roger, Chad Nusbaum & Iñaki Ruiz-Trillo (2013)
The Capsaspora genome reveals a complex unicellular prehistory of animals.
Nature Communications 4: 2325 (2013)
José M. Martín-Durán, Alex de Mendoza, Arnau Sebé-Pedrós, Iñaki Ruiz-Trillo & Andreas Hejnol (2013)
A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins.
Genome Biology and Evolution 5(7):1435-42
Xavier Grau-Bové, Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo (2013)
A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages.
Genome Biology and Evolution 5(5):833-47
Access alignments
Javier del Campo & Iñaki Ruiz-Trillo (2013)
Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts.
Molecular Biology and Evolution 30(4): 802-805
Access alignment
Alex de Mendoza, Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo (2013)
El origen de la multicelularidad.
Investigación y Ciencia Febrero 2013 pp.32-39
Hiroshi Suga & Iñaki Ruiz-Trillo (2013)
Development of ichthyosporeans sheds light on the origin of metazoan multicellularity.
Developmental Biology 377(1):284-292
Jordi Paps, Luis A. Medina-Chacón, Wyth Marshall, Hiroshi Suga & Iñaki Ruiz-Trillo (2013)
Molecular phylogeny of Unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of opisthokonts.
Protist 164(1):2-12
Concatenated alignment
2012
Kira P. Schultheiss, Hiroshi Suga, Iñaki Ruiz-Trillo & W. Todd Miller (2012)
Lack of Csk-mediated negative regulation in a unicellular Src kinase.
Biochemistry 51 (41), pp 8267–8277
Hiroshi Suga, Michael Dacre, Alex de Mendoza, Kamran Shalchian-Tabrizi, Gerard Manning & Iñaki Ruiz-Trillo (2012)
Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases.
Science Signaling 5 (222), ra35
Listen to Science Signaling Podcast
Naiara Rodríguez-Ezpeleta, David Moreira, Iñaki Ruiz-Trillo (2012)
“Protistas”:Amoebozoa, Rhizaria, Excavata, Hacrobia, Heterokonta y Alveolata.
In “El árbol de la vida: sistemática y evolución de los seres vivos”. Zardoya R. & Vargas P. eds.
Iñaki Ruiz-Trillo (2012)
Eucariotas.
In “El árbol de la vida: sistemática y evolución de los seres vivos”. Zardoya R. & Vargas P. eds.
Marta Riutort, Jordi Paps, Iñaki Ruiz-Trillo (2012)
Bilaterales.
In “El árbol de la vida: sistemática y evolución de los seres vivos”. Zardoya R. & Vargas P. eds.
Arnau Sebé-Pedrós, Yonggang Zheng, Iñaki Ruiz-Trillo & Duojia Pan (2012)
Premetazoan origin of the Hippo signaling pathway.
Cell Reports 1 (1): 13-20
Access sequences
Guifré Torruella, Romain Derelle, Jordi Paps, B. Franz Lang, Andrew J Roger, Kamran Shalchian-Tabrizi & Iñaki Ruiz-Trillo (2012)
Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single copy protein domains.
Molecular Biology and Evolution 29(2): 531-544
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John D. L. Shadwick & Iñaki Ruiz-Trillo (2012)
A genomic survey shows that the haloarchaeal type Tyrosyl-Synthetase is not a Synapomorphy of Opisthokonts.
European Journal of Protistology 48(1):89-93
2011
Alex de Mendoza & Iñaki Ruiz-Trillo (2011)
New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference.
Evodevo 2(1):22
Agatha Schlüter, Iñaki Ruiz-Trillo & Aurora Pujol (2011)
Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation.
PLoS ONE 6(7): e21989
Alex de Mendoza & Iñaki Ruiz-Trillo (2011)
The mysterious Evolutionary Origin for the GNE gene and the root of Bilateria.
Molecular Biology and Evolution 28(11): 2987-91
Access alignments
Susan Young, D. Diolaiti, M. Conacci-Sorrell, Iñaki Ruiz-Trillo, R. M. Eisenman & Nicole King (2011)
Premetazoan Ancestry of the Myc-Max Network.
Molecular Biology and Evolution 28(10): 2961-71
Arnau Sebé-Pedrós, Alex de Mendoza, B. Franz Lang, Bernie M. Degnan & Iñaki Ruiz-Trillo (2011)
Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki.
Molecular Biology and Evolution 28(3): 1241-54
2010
Maria José Barberà*, Iñaki Ruiz-Trillo*, Julia Y. A. Tufts, Bery Amandine, Jeffrey D. Silberman & Andrew J. Roger (*co-authors) (2010)
Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties.
Eukaryotic Cell 9(12):1913-24
Jordi Paps & Iñaki Ruiz-Trillo (2010)
Animals and their unicellular ancestors.
In “Encyclopedia of Life Sciences” 2010. John Wiley & Sons, Ltd: Chichester.
Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo (2010)
The integrin-mediated adhesion complex: cooption of signaling systems at the dawn of Metazoa.
Communicative & Integrative Biology 3:5 475-477
Alex de Mendoza, Hiroshi Suga & Iñaki Ruiz-Trillo (2010)
Evolution of the MAGUK protein gene family in premetazoan lineages.
BMC Evolutionary Biology 10(1):93
Alignments
Arnau Sebé-Pedrós, Andrew J. Roger, Franz B. Lang, Nicole King & Iñaki Ruiz-Trillo (2010)
Ancient origin of integrin-mediated adhesion and signaling machinery.
Proceedings National Academic of Sciences USA 107(22): 10142-10147
Iñaki Ruiz-Trillo (2010)
Animales y sus ancestros unicelulares. Una visión filogenómica.
In “Adaptación y Evolución. 150 años después del Origen de las Especies” SESBE 2009. Dopazo. & Navarro. eds, Obrapropia Editorial, Valencia.
2009
Guifré Torruella, Hiroshi Suga, Marta Riutort, Juli Peretó & Iñaki Ruiz-Trillo (2009)
The evolutionary history of lysine biosynthesis pathways within eukaryotes.
Journal of Molecular Evolution 69(3): 240-248
Access alignments
2008
Iñaki Ruiz-Trillo, Andrew J. Roger, Gertraud Burger, Michael W. Gray & B. Franz Lang (2008)
A phylogenomic investigation into the origin of Metazoa.
Molecular Biology and Evolution 25 (4): 664-672
Access alignments
E. Bapteste, E. Susko, J. Leigh, I. Ruiz-Trillo, J. Bucknam & W. F. Doolittle (2008)
Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny.
Molecular Biology and Evolution 25(1): 83-91
2007
Iñaki Ruiz-Trillo, Gertraud Burger, Peter W. H. Holland, Nicole King, B. Franz Lang, Andrew J. Roger & Michael W. Gray (2007)
The origins of multicellularity: a multi-taxon genome initiative.
Trends in Genetics 23(3): 113-118
Maria J. Barberà, Iñaki Ruiz-Trillo, Jessica Leigh, Laura A. Hug & Andrew J. Roger (2007)
The diversity of mitochondrion-related organelles amongst eukaryotic microbes.
In “Origins of Mitochondria and Hydrogenosomes”. Martin W. ed., Springer, Heidelberg.
2006
Iñaki Ruiz-Trillo, Christopher E. Lane, John M. Archibald & Andrew J. Roger (2006)
Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica.
Journal of Eukaryotic Microbiology 53(5): 1-6
Sina M. Adl, Iñaki Ruiz-Trillo & Melanie L. Wilson (2006)
Observations on a Geocentrophora sp. (Lecitoepitheliata) flatworm from forest soils in Nova Scotia.
Journal of Natural History 40 (23-24): 1381-1387
2004
Iñaki Ruiz-Trillo, Yuji Inagaki, Lesley A. Davis, Sigmund Sperstad, Bjarne Landfald & Andrew J. Roger (2004)
Capsaspora owczarzaki is an independent opisthokont lineage.
Current Biology 14: R946-R947
Iñaki Ruiz-Trillo, Marta Riutort, H. Matthew Fourcade, Jaume Baguñà & Jeffrey L. Boore (2004)
Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes.
Molecular Phylogenetics and Evolution 33: 321- 332, 2004
2002
I. Ruiz-Trillo, J. Paps, M. Loukota, C. Ribera, U. Jondelius, J. Baguñà & M. Riutort (2002)
A phylogenetic analysis of Myosin Heavy Chain type II sequences corroborates Acoela and Nemertodermatida are basal bilaterians.
Proceedings National Academic of Sciences USA 99:11246-11251
Jaume Baguñà, Iñaki Ruiz-Trillo, Jordi Paps & Marta Riutort (2002)
Origen y evolución de los ejes corporales y la simetría bilateral en animales.
In “Evolución: la base de la Biología” (M.Soler ed.), Proyecto Sur Editorial.
U. Jondelius, I. Ruiz-Trillo, J. Baguñà & M. Riutort (2002)
The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes.
Zoologica Scripta 31: 201-215
2001
Iñaki Ruiz-Trillo (2001)
Acoela.
In “McGraw-Hill Encyclopedia of Science and Technology, 2001 Yearbook of Science & Technology”. McGraw-Hill, New York.
J. Baguñà, I. Ruiz-Trillo, J. Paps, M. Loukota, C.s Ribera, U. Jondelius & M. Riutort (2001)
The first bilaterian organisms: simple or complex? New molecular evidence.
International Journal of Developmental Biology 45: S133-S134
2000
J. Baguñà, S. Carranza, J. Paps, I. Ruiz-Trillo & M. Riutort (2000)
Molecular taxonomy and phylogeny of Tricladida.
In “Interrelationships of the Platyhelminthes”, Littlewood & Bray Ed., Taylor & Francis, London.
1999
I. Ruiz-Trillo, M. Riutort, D. T. J. Littlewood, E. A. Herniou & J. Baguñà (1999)
Acoel flatworms: earliest extant bilaterian metazoans, not members of the Platyhelminthes.
Science 283: 1919-1923
