Multicellgenome Lab
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
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
López-Panadès E, Casacuberta E. 2016. NAP-1, Nucleosome assembly protein 1, a histone chaperone involved in Drosophila telomeres. Insect Biochemistry and Molecular Biology, 70:111-115. DOI:10.1016/j.ibmb.2015.11.011
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
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
López-Panadès E, Gavis ER, Casacuberta E. 2015. Specific localization of the Drosophila telomere transposon proteins and RNAs, give insight in their behavior, control and telomere biology in this organism. PLoS ONE, 10(6):1-17. DOI:10.1371/journal.pone.0128573
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
Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF, Eliáš M. 2015. Bacterial proteins pinpoint a single eukaryotic root. Proceedings of the National Academy of Sciences of the United States of America, 112(7):E693-E699. DOI:10.1073/pnas.1420657112
de Mendoza A, Suga H, Permanyer J, Irimia M, Ruiz-Trillo I. 2015. Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. eLife, 4:1-26. DOI:10.7554/elife.08904
del Campo J, Mallo D, Massana R, de Vargas C, Richards TA, Ruiz-Trillo I. 2015. Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing. Environmental Microbiology, 17(9):3195-3207. DOI:10.1111/1462-2920.12759
Alzayady KJ, Sebe-Pedros A, Chandrasekhar R, Wang L, Ruiz-Trillo I, Yule DI. 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. DOI:10.1093/molbev/msv098
Suga H, Torruella G, Burger G, Brown MW, Ruiz-Trillo I. 2014. Earliest holozoan expansion of phosphotyrosine signaling. Molecular Biology and Evolution, 31(3):517-528. DOI:10.1093/molbev/mst241
Sebé-Pedrós A, Grau-Bové X, Richards TA, Ruiz-Trillo I. 2014. Evolution and classification of myosins, a paneukaryotic whole-genome approach. Genome Biology and Evolution, 6(2):290-305. DOI:10.1093/gbe/evu013
Schultheiss KP, Craddock BP, Suga H, Miller WT. 2014. Regulation of Src and Csk nonreceptor tyrosine kinases in the filasterean Ministeria vibrans. Biochemistry. 2014;53(8):1320-1329. DOI:10.1021/bi4016499
Desvoyes B, De Mendoza A, Ruiz-Trillo I, Gutierrez C. 2014. Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. Journal of Experimental Botany, 65(10):2657-2666. DOI:10.1093/jxb/ert411
De Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I. 2014. The evolution of the GPCR signaling system in eukaryotes: Modularity, conservation, and the transition to metazoan multicellularity. Genome Biology and Evolution, 6(3):606-619. DOI:10.1093/gbe/evu038
De Mendoza A, Ruiz-Trillo I. 2014. Forward genetics for back-in-time questions. eLife, 3:1-3. DOI:10.7554/eLife.05218
Del Campo J, Sieracki ME, Molestina R, Keeling P, Massana R, Ruiz-Trillo I. 2014. The others: Our biased perspective of eukaryotic genomes. Trends in Ecology and Evolution, 29(5):252-259. DOI:10.1016/j.tree.2014.03.006
Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I. 2013. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nature Communications, 4:1-9. DOI:10.1038/ncomms3325
Suga H, Ruiz-Trillo I. 2013. Development of ichthyosporeans sheds light on the origin of metazoan multicellularity. Developmental Biology, 377(1):284-292. DOI:10.1016/j.ydbio.2013.01.009
Silva-Sousa R, Casacuberta E. 2013. The JIL-1 kinase affects telomere expression in the different telomere domains of Drosophila. PLoS ONE, 8(11):1-8. DOI:10.1371/journal.pone.0081543
Silva-Sousa R, Varela MD, Casacuberta E. 2013. The Putzig partners DREF, TRF2 and KEN are involved in the regulation of the Drosophila telomere retrotransposons, HeT-A and TART. Mobile DNA, 4(1):1-8. DOI:10.1186/1759-8753-4-18
Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I. 2013. Early evolution of the T-box transcription factor family. Proceedings of the National Academy of Sciences of the United States of America, 110(40):16050-16055. DOI:10.1073/pnas.1309748110
Sebé-Pedrós A, Burkhardt P, Sánchez-Pons N, Fairclough SR, Lang BF, King N, Ruiz-Trillo I. 2013. Insights into the origin of metazoan filopodia and microvilli. Molecular Biology and Evolution, 30(9):2013-2023. DOI:10.1093/molbev/mst110
Sebé-Pedrós A, Irimia M, Del Campo J, Parra-Acero H, Russ C, Nusbaum C, Blencowe BJ, Ruiz-Trillo I. 2013. Regulated aggregative multicellularity in a close unicellular relative of metazoa. eLife, 2013(2):1-20. DOI:10.7554/eLife.01287
Roldán M, Ramírez M, Del Campo J, Hernández-Mariné M, Komárek J. 2013. Chalicogloea cavernicola gen. nov., sp. nov.(chroococcales, cyanobacteria), from low-lightaerophytic environments: Combined molecular,phenotypic and ecological criteria. International Journal of Systematic and Evolutionary Microbiology, 63(PART6):2326-2333. DOI:10.1099/ijs.0.045468-0
Paps J, Medina-Chacón LA, Marshall W, Suga H, Ruiz-Trillo I. 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. DOI:10.1016/j.protis.2012.09.002
Martín-Durán JM, De Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I, Hejnol A. 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):1435-1442. DOI:10.1093/gbe/evt102
Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I. 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):833-847. DOI:10.1093/gbe/evt052
De Mendoza A, Sebé-Pedrós A, Šestak MS, Matejcic M, Torruella G, Domazet-Loso T, Ruiz-Trillo I. 2013. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proceedings of the National Academy of Sciences of the United States of America, 110(50). DOI:10.1073/pnas.1311818110
Del Campo J, Ruiz-Trillo I. 2013. Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts. Molecular Biology and Evolution, 30(4):802-805. DOI:10.1093/molbev/mst006
Del Campo J, Balagué V, Forn I, Lekunberri I, Massana R. 2013. Culturing Bias in Marine Heterotrophic Flagellates Analyzed Through Seawater Enrichment Incubations. Microbial Ecology, 66(3):489-499. DOI:10.1007/s00248-013-0251-y
Casacuberta E, González J. 2013. The impact of transposable elements in environmental adaptation. Molecular Ecology, 22(6):1503-1517. DOI:10.1111/mec.12170
Torruella G, Derelle R, Paps J, Lang BF, Roger AJ, Shalchian-Tabrizi K, Ruiz-Trillo I. 2012. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Molecular Biology and Evolution. 2029(2):531-544. DOI:10.1093/molbev/msr185
Suga H, Dacre M, De Mendoza A, Shalchian-Tabrizi K, Manning G, Ruiz-Trillo I. 2012. Genomic survey of premetazoans shows deep conservation of cytoplasmic tyrosine kinases and multiple radiations of receptor tyrosine kinases. Science Signaling, 5(222):26-28. DOI:10.1126/scisignal.2002733
Silva-Sousa R, López-Panadès E, Piñeyro D, Casacuberta E. 2012. The Chromosomal Proteins JIL-1 and Z4/Putzig Regulate the Telomeric Chromatin in Drosophila melanogaster. PLoS Genetics, 8(12). DOI:10.1371/journal.pgen.1003153
Shadwick JDL, Ruiz-Trillo I. 2012. A genomic survey shows that the haloarchaeal type tyrosyl tRNA synthetase is not a synapomorphy of opisthokonts. European Journal of Protistology, 48(1):89-93. DOI:10.1016/j.ejop.2011.10.003
Sebe-Pedrs A, Zheng Y, Ruiz-Trillo I, Pan D. 2012. Premetazoan Origin of the Hippo Signaling Pathway. Cell Reports, 1(1):13-20. DOI:10.1016/j.celrep.2011.11.004
Schultheiss KP, Suga H, Ruiz-Trillo I, Miller WT. 2012. Lack of Csk-mediated negative regulation in a unicellular Src kinase. Biochemistry, 51(41):8267-8277. DOI:10.1021/bi300965h
Petit N, Piñeyro D, López-Panadès E, Casacuberta E, Navarro A. 2012. HeT-A_pi1, a piRNA target sequence in the Drosophila telomeric retrotransposon HeT-A, is extremely conserved across copies and species. PLoS ONE, 7(5):1-11. DOI:10.1371/journal.pone.0037405
Piñeyro D, López-Panadès E, Lucena-Pérez M, Casacuberta E. 2011. Transcriptional analysis of the HeT-A retrotransposon in mutant and wild type stocks reveals high sequence variability at Drosophila telomeres and other unusual features. BMC Genomics, 12. DOI:10.1186/1471-2164-12-573
de Mendoza A, Ruiz-Trillo I. 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):2-4. DOI:10.1186/2041-9139-2-22