Multicellgenome

Salamanca-Díaz DA, Horkan HR, García-Castro H, Emili E, Salinas-Saavedra M, Pérez-Posada A, Rossi ME, Álvarez-Presas M, Mac Gabhann R, Hillenbrand P, Febrimarsa, Curantz C, Weavers PK, Lund-Ricard Y, Förg T, Michaca MH, Sanders SM, Kenny NJ, Paps J, Frank U, Solana J. 2025. The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality. Nature Communications. 16(1), 2121. DOI: 10.1038/s41467-025-57168-z

García-Bodelón Á, Baković N, Cano E, Useros F, Lara E, & González-Miguéns R. 2025. Predators in the Dark: Metabarcoding Reveals Arcellinida Communities Associated with Bat Guano, Endemic to Dinaric Karst in Croatia. Microbial Ecology. 87(1):166. DOI: 10.1007/s00248-024-02483-z

Shabardina V, Dharamshi JE, Ara PS, Antó M, Bascón FJ, Suga H, Marshall W, Scazzocchio C, Casacuberta E, Ruiz-Trillo I. 2024. Ichthyosporea: a window into the origin of animals. Communications Biology, 7(1):915. DOI:10.1038/s42003-024-06608-5

Richards TA, Eme L, Archibald JM, Leonard G, Coelho SM, de Mendoza A, Dessimoz C, Dolezal P, Fritz-Laylin LK, Gabaldón T, Hampl V, Kops GJPL, Leger MM, Lopez-Garcia P, McInerney JO, Moreira D, Muñoz-Gómez SA, Richter DJ, Ruiz-Trillo I, Santoro AE, Sebé-Pedrós A, Snel B, Stairs CW, Tromer EC, van Hooff JJE, Wickstead B, Williams TA, Roger AJ, Dacks JB, Wideman JG. 2024. Reconstructing the last common ancestor of all eukaryotes. PLOS Biology, 22(11):e3002917. DOI:10.1371/journal.pbio.3002917

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 Reports, 43(3):113791. DOI:10.1016/j.celrep.2024.113791

Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. 2023. On the origin and evolution of RNA editing in metazoans. Cell Reports, 42(2):112112. DOI:10.1016/j.celrep.2023.112112

Shabardina V, Charria PR, Saborido GB, Diaz-Mora E, Cuenda A, Ruiz-Trillo I, Sanz-Ezquerro JJ. 2023. Evolutionary analysis of p38 stress-activated kinases in unicellular relatives of animals suggests an ancestral function in osmotic stress. Open Biology, 13(1):2022.04.24.489300. DOI:10.1098/rsob.220314.

Ruiz-Trillo I, Kin K, Casacuberta E. 2023. The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. Annual Review of Microbiology, 77(1). DOI:10.1146/annurev-micro-032421-120023

Ros-Rocher N, Kidner RQ, Gerdt C, Davidson WS, Ruiz-Trillo I, Gerdt JP. 2023. Chemical factors induce aggregative multicellularity in a close unicellular relative of animals. Proceedings of the National Academy of Sciences, 120(18):2017. DOI:10.1073/pnas.2216668120

Mitsi K, Richter DJ, Arroyo AS, López-Escardó D, Antó M, Oterino AG, Ruiz-Trillo I. 2023. Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding. Scientific Reports, 13(1):3119. DOI:10.1038/s41598-023-30228-4

Boeynaems S, Dorone Y, Zhuang Y, Shabardina V, Huang G, Marian A, Kim G, Sanyal A, Şen NE, Griffith D, Docampo R, Lasker K, Ruiz-Trillo I, Auburger G, Holehouse AS, Kabashi E, Lin Y, Gitler AD. 2023. Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates. Molecular Cell, 83(12):2020-2034. DOI:10.1016/j.molcel.2023.05.025

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

Chafino S, Ureña E, Casanova J, Casacuberta E, Franch-Marro X, Martín D. 2019. Upregulation of E93 Gene Expression Acts as the Trigger for Metamorphosis Independently of the Threshold Size in the Beetle Tribolium castaneum. Cell Reports, 27(4):1039-1049. DOI:10.1016/j.celrep.2019.03.094.

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

Chafino S, López-Escardó D, Benelli G, Kovac H, Casacuberta E, Franch-Marro X, Kathirithamby J, Martín D. 2018. Differential expression of the adult specifier E93 in the strepsipteran Xenos vesparum Rossi suggests a role in female neoteny. Scientific Reports, 8(1):1-11. DOI:10.1038/s41598-018-32611-y

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