Research lines

The goal of this lab is to understand the origin of animal multicellularity from a unicellular ancestor. To this end, the genomes of animals’ closest unicellular relatives are obtained in order to perform comparative and functional genomics. Moreover, the Multicellgenome lab is working on the development of genetic tools in two close unicellular relatives of animals with the purpose of establishing them as model organisms for addressing the origin of Metazoa. This will enable the elucidation of the ancestral function of the genes involved in multicellularity and offer insight into how they were co-opted.

Lab website: Multicellgenome Lab

Principal Investigator

Iñaki Ruiz Trillo

Ruiz Trillo, Iñaki
ICREA Research Professor
Multicell Genome Lab

Current members

Meritxell Antó Subirats

Antó Subirats, Meritxell
Laboratory technician
Multicell Genome Lab

Gonzalo Bercedo Saborido

Bercedo Saborido, Gonzalo
Predoctoral Researcher
Multicellgenome Lab

Stuart Donachie

Donachie, Stuart
Visitors
Multicellgenome Lab

Anna Karnkowska

Karnkowska, Anna
Visitors
Multicellgenome

KORYU KIN

KIN, KORYU

MICHELLE MARIE LEGER

LEGER, MICHELLE MARIE

Victoria Shabardina

Shabardina, Victoria
Postdoctoral Researcher
Evolution of the Eukaryote Genome Lab

Lukasz Sobala

Sobala, Lukasz
visitors
Multicellgenome

Patricia Suarez Ara

Suarez Ara, Patricia
Predoctoral Researcher
Multicell Genome Lab

Ongoing projects

Publications

Urrutia A, Mitsi K, Foster R, Ross S, Carr M, Ward GM, van Aerle R, Marigomez I, Leger MM, Ruiz-Trillo I, Feist SW, Bass D. 2022. Txikispora philomaios n. sp., n. g., a Micro‐Eukaryotic Pathogen of Amphipods, Reveals Parasitism and Hidden Diversity in Class Filasterea. Journal of Eukaryotic Microbiology, 69(2). DOI:10.1111/jeu.12875

Ocaña-Pallarès E, Williams TA, López-Escardó D, Arroyo AS, Pathmanathan JS, Bapteste E, Tikhonenkov DV, Keeling PJ, Szöllősi GJ, Ruiz-Trillo I. 2022. Divergent genomic trajectories predate the origin of animals and fungi. Nature, 609(7928):747-753. DOI:10.1038/s41586-022-05110-4

Leger MM, Ros-Rocher N, Najle SR, Ruiz-Trillo I. 2022. Rel/NF-κB transcription factors emerged at the onset of opisthokonts. Genome Biology and Evolution, 14(1). DOI:10.1093/gbe/evab289

Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. 2022. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nature Ecology & Evolution, 6(7):1007-1023. DOI:10.1038/s41559-022-01771-6

Dudin O, Wielgoss S, New AM, Ruiz-Trillo I. 2022. Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals. PLOS Biology, 20(3):e3001551. DOI:10.1371/journal.pbio.3001551

Ros-Rocher N, Pérez-Posada A, Leger MM, Ruiz-Trillo I. 2021. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biology, 11(2). DOI: 10.1098/rsob.200359. 

Kożyczkowska A, Najle SR, Ocaña-Pallarès E, Aresté C, Shabardina V, Ara PS, Ruiz-Trillo I, Casacuberta E. 2021. Stable transfection in protist Corallochytrium limacisporum identifies novel cellular features among unicellular animals relatives. Current Biology, 31(18):4104-4110. DOI:10.1016/j.cub.2021.06.061

Guberovic I, Hurtado-Bagès S, Rivera-Casas C, Knobloch G, Malinverni R, Valero V, Leger MM, García J, Basquin J, Gómez de Cedrón M, Frigolé-Vivas M, Cheema MS, Pérez A, Ausió J, Ramírez de Molina A, Salvatella X, Ruiz-Trillo I, Eirin-Lopez JM, Ladurner AG, Buschbeck M. 2021. Evolution of a histone variant involved in compartmental regulation of NAD metabolism. Nature Structural & Molecular Biology, 28(12):1009-1019. DOI:10.1038/s41594-021-00692-5

Ruiz-Trillo I, de Mendoza A. 2020. Towards understanding the origin of animal development. Development, 147(23):1-7. DOI:10.1242/dev.192575

Pérez-Posada A, Dudin O, Ocaña-Pallarès E, Ruiz-Trillo I, Ondracka A. 2020. Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery. PLOS Genetics, 16(3). DOI: 10.1371/journal.pgen.1008584

Parra-Acero H, Harcet M, Sánchez-Pons N, Casacuberta E, Brown NH, Dudin O, Ruiz-Trillo I. 2020. Integrin-Mediated Adhesion in the Unicellular Holozoan Capsaspora owczarzaki. Current Biology, 30(21):4270-4275. DOI: 10.1016/j.cub.2020.08.015

Ocaña-Pallarès E, Vergara Z, Desvoyes B, Tejada-Jimenez M, Romero-Jurado A, Galván A, Fernández E, Ruiz-Trillo I, Gutierrez C. 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. DOI:10.1093/gbe/evaa011

Lu Y, Ocaña-Pallarès E, López-Escardó D, Dennis SR, Monaghan MT, Ruiz-Trillo I, Spaak P, Wolinska J.  2020. Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes. Molecular Phylogenetics and Evolution, 151(106891). DOI: 10.1016/j.ympev.2020.106891

Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M Jr, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods, 17(5):481-494. DOI: 10.1038/s41592-020-0796-x.

da Silva A, Nobre H, Sampaio L, Nascimento B do, da Silva C, de Andrade Neto JB, Manresa Á, Pinazo A, Cavalcanti B, de Moraes MO, Ruiz-Trillo I, Antó M, Morán C, Pérez L. 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). DOI: 10.1016/j.colsurfb.2020.111148

Arroyo AS, Iannes R, Bapteste E, Ruiz-Trillo I. 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. DOI: 10.1093/gbe/evaa117.

Rafels-Ybern À, Torres AG, Camacho N, Herencia-Ropero A, Roura Frigolé H, Wulff TF, Raboteg M, Bordons A, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L. 2019. 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. DOI:10.1093/molbev/msy245

O’Malley MA, Leger MM, Wideman JG, Ruiz-Trillo I. 2019. Concepts of the last eukaryotic common ancestor. Nature Ecology and Evolution, 3(3):338-344. DOI:10.1038/s41559-019-0796-3

Ocaña-Pallarès E, Najle SR, Scazzocchio C, Ruiz-Trillo I. 2019. Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway. PLOS Genetics, 15(2). DOI:10.1371/journal.pgen.1007986

Mitsi K, Arroyo AS, Ruiz-Trillo I. 2019. A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades. Biology Letters, 15(9). DOI:10.1098/rsbl.2019.0182

López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, Ruiz-Trillo I. 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: Biological Sciences, 374(1786). DOI:10.1098/rstb.2019.0088

Dudin O, Ondracka A, Grau-Bové X, Haraldsen AA, Toyoda A, Suga H, Bråte J, Ruiz-Trillo I. 2019. A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife, 8:1-26. DOI:10.7554/eLife.49801

Denbo S, Aono K, Kai T, Yagasaki R, Ruiz-Trillo I, Suga H. 2019. Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome. Development Growth and Differentiation, 61(1):34-42. DOI:10.1111/dgd.12587

Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, Del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology, 66(1):4-119. DOI: 10.1111/jeu.12691

Waller RF, Cleves PA, Rubio-Brotons M, Woods A, Bender SJ, Edgcomb V, Gann ER, Jones AC, Teytelman L, von Dassow P, Wilhelm SW, Collier JL. 2018. Strength in numbers: Collaborative science for new experimental model systems. PLoS Biology. 2018;16(7):1-10. DOI:10.1371/journal.pbio.2006333

Rafels-Ybern À, Torres AG, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L. 2018.  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. DOI:10.1080/15476286.2017.1358348

Parra-Acero H, Ros-Rocher N, Perez-Posada A, Kożyczkowska A, Sánchez-Pons N, Nakata A, Suga H, Najle SR, Ruiz-Trillo I. 2018. Transfection of Capsaspora owczarzaki, a close unicellular relative of animals. Development (Cambridge), 145(10):1-8. DOI:10.1242/dev.162107

Ondracka A, Dudin O, Ruiz-Trillo I. 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. DOI:10.1016/j.cub.2018.04.074

Merlini L, Khalili B, Dudin O, Michon L, Vincenzetti V, Martin SG. 2018. Inhibition of Ras activity coordinates cell fusion with cell-cell contact during yeast mating. Journal of Cell Biology, 217(4):1467-1483. DOI:10.1083/jcb.201708195

López-Escardó D, Paps J, De Vargas C, Massana R, Ruiz-Trillo I, Del Campo J. 2018. Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Scientific Reports, 8(1):1-14. DOI:10.1038/s41598-018-27509-8

López-Escardó D, López-García P, Moreira D, Ruiz-Trillo I, Torruella G. 2018. Parvularia atlantis gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta). Journal of Eukaryotic Microbiology, 65(2):170-179. DOI:10.1111/jeu.12450

Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. 2018. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides. Open Biology, 8(1):170184. DOI:10.1098/rsob.170184

Grau-Bové X, Ruiz-Trillo I, Irimia M. 2018. Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. Genome Biology, 19(1):135. DOI:10.1186/s13059-018-1499-9

Ćetković H, Bosnar MH, Perina D, Mikoč A, Deželjin M, Belužić R, Bilandžija H, Ruiz-Trillo I, Harcet M. 2018. Characterization of a group i Nme protein of Capsaspora owczarzaki - A close unicellular relative of animals. Laboratory Investigation, 98(3):304-314. DOI:10.1038/labinvest.2017.134

Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K. 2018. Unicellular Origin of the Animal MicroRNA Machinery. Current Biology, 28(20):3288-3295. DOI:10.1016/j.cub.2018.08.018

Arroyo AS, López-Escardó D, Kim E, Ruiz-Trillo I, Najle SR. 2018. Novel diversity of deeply branching holomycota and unicellular holozoans revealed by metabarcoding in Middle Paraná River, Argentina. Frontiers in Ecology and Evolution,  6:1-17. DOI:10.3389/fevo.2018.00099

Sebé-Pedrós A, Ruiz-Trillo I. 2017. Evolution and Classification of the T-Box Transcription Factor Family. Current Topics in Developmental Biology, Vol 122:1-26. DOI:10.1016/bs.ctdb.2016.06.004

Sebé-Pedrós A, Degnan BM, Ruiz-Trillo I. 2017. The origin of Metazoa: A unicellular perspective. Nature Reviews Genetics, 18(8):498-512. DOI:10.1038/nrg.2017.21

Ferrer-Bonet M, Ruiz-Trillo I. 2017. Capsaspora owczarzaki. Current Biology, 27(17):R829-R830. DOI:10.1016/j.cub.2017.05.074

Sebé-Pedrós A, Peña MI, Capella-Gutiérrez S, Antó M, Gabaldón T, Ruiz-Trillo I, Sabidó E. 2016. High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation. Developmental Cell, 39(2):186-197. DOI:10.1016/j.devcel.2016.09.019

Sebé-Pedrós A, Ballaré C, Parra-Acero H, Chiva C, Tena JJ, Sabidó E, Gómez-Skarmeta JL, Di Croce L, Ruiz-Trillo I. 2016. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell, 165(5):1224-1237. DOI:10.1016/j.cell.2016.03.034

Ruiz-Trillo I, Paps J. 2016. Acoelomorpha: earliest branching bilaterians or deuterostomes?. Organisms Diversity and Evolution, 16(2):391-399. DOI:10.1007/s13127-015-0239-1

O’Malley MA, Wideman JG, Ruiz-Trillo I. 2016. Losing Complexity: The Role of Simplification in Macroevolution. Trends in Ecology and Evolution, 31(8):608-621. DOI:10.1016/j.tree.2016.04.004

Najle SR, Molina MC, Ruiz-Trillo I, Uttaro AD. 2016. Sterol metabolism in the filasterean Capsaspora owczarzaki has features that resemble both fungi and animals. Open Biology, 6(7). DOI:10.1098/rsob.160029

Gold DA, Grabenstatter J, De Mendoza A, Riesgo A, Ruiz-Trillo I, Summons RE. 2016. Sterol and genomic analyses validate the sponge biomarker hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 113(10):2684-2689. DOI:10.1073/pnas.1512614113

Esquerdo M, Grau-Bové X, Garanto A, Toulis V, Garcia-Monclús S, Millo E, López-Iniesta MJ, Abad-Morales V, Ruiz-Trillo I, Marfany G. 2016. Expression Atlas of the Deubiquitinating Enzymes in the Adult Mouse Retina, Their Evolutionary Diversification and Phenotypic Roles. PLoS ONE, 11(3):1-18. DOI:10.1371/journal.pone.0150364

Arroyo AS, López-Escardó D, de Vargas C, Ruiz-Trillo I. 2016. Hidden diversity of Acoelomorpha revealed through metabarcoding. Biology Letters, 12(9):20160674. DOI: 10.1098/rsbl.2016.0674.

Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I. 2015. Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi. Current Biology, 25(18):2404-2410. DOI:10.1016/j.cub.2015.07.053

Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I. 2015. The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin. Molecular Biology and Evolution, 32(3):726-739. DOI:10.1093/molbev/msu334

Grau-Bové X, Ruiz-Trillo I, Rodriguez-Pascual F. 2015. Origin and evolution of lysyl oxidases. Scientific Reports, 5:1-11. DOI:10.1038/srep10568

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