Departament de Genètica 


EVOLUTION AND
 DEVELOPMENT


Jaume Baguñà
Cristian Cañestro
Jordi Garcia
Pere Martínez
Marta Riutort
Iñaki Ruiz-Trillo
Joan Antoni Vela

IÑAKI RUIZ-TRILLO


contact
bio
research
publications


SELECTED PUBLICATIONS



Articles

Arnau Sebé-Pedrós, Manuel Irimia, Javier del Campo, Helena Parra-Acero, Carsten Russ, Chad Nusbaum, Benjamin J. Blencowe & Iñaki Ruiz-Trillo. Regulated aggregative multicellularity in a close unicellular relative of Metazoa. eLife (in press)

Hiroshi Suga, Guifré Torruella, Gertraud Burger, Matthew W. Brown & Iñaki Ruiz-Trillo. Earliest holozoan expansion of phosphotyrosine signaling. Molecular Biology and Evolution (in press)

Bénédicte Desvoyes, Alex de Mendoza, Iñaki Ruiz-Trillo and Crisanto Gutierrez. Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. Journal of Experimental Botany (in press)

Alex de Mendoza, Arnau Sebé-Pedrós, Martin Sebastijan Šestak, Marija Matejčić, Guifré Torruella, Tomislav Domazet-Lošo & Iñaki Ruiz-Trillo. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proceedings National Academic of Sciences USA (in press)

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. Early evolution of the T-box transcription factor family. Proceedings National Academic of Sciences USA 110(40):16050-5.

Arnau Sebé-Pedrós, Pawel Burkhardt, Núria Sánchez-Pons, Stephen R. Fairclough, B. Franz Lang, Nicole King & IñakiRuiz-Trillo.  Insights into the origin of metazoan filopodia and microvilli. Molecular Biology and Evolution 30(9):2013-23.

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. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nature Communications 4: 2325 doi: 10.1038/ncomms3325 (2013).

José M. Martín-Durán, Alex de Mendoza, Arnau Sebé-Pedrós, Iñaki Ruiz-Trillo & Andreas Hejnol.  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.  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. doi: 10.1093/gbe/evt052.

Javier del Campo & Iñaki Ruiz-Trillo.  Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts. Molecular Biology and Evolution 30(4): 802-805.

Alex de Mendoza, Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo.  El origen de la multicelularidad. Investigación y Ciencia, Febrero 2013 pp.32-39.

Hiroshi Suga & Iñaki Ruiz-Trillo. Development of ichthyosporeans sheds light on the origin of metazoan multicellularity. Developmental Biology 377, 284-292.

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.

Arnau Sebé-Pedrós, Yonggang Zheng, Iñaki Ruiz-Trillo & Duojia Pan. (2012) Premetazoan origin of the Hippo signaling pathway. Cell Reports 1(1): 13-20. doi:10.1016/j.cel- rep.2011.11.004

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 [DOI: 10.1126/scisignal.2002733]

Jordi Paps, Luis A. Medina-Chacón, Wyth Marshall, Hiroshi Suga & Iñaki Ruiz-Trillo. Molecular phylogeny of Unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of opisthokonts. Protist 164(1):2-12.

Kira P. Schultheiss, Hiroshi Suga, Iñaki Ruiz-Trillo & W. Todd Miller. Lack of Csk-mediated negative regulation in a unicellular Src kinase. Biochemistry 51 (41), pp 8267–8277.

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. doi:10.1371/journal.pone.0021989

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.

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.

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.

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): 1241-1254

Maria José Barberà*, Iñaki Ruiz-Trillo*, Julia Y. A. Tufts, Bery Amandine, Jeffrey D. Silberman & Andrew J. Roger. (2010) Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties. Eukaryotic Cell 9: 1913-1924 (*co-authors)

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

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 Academy of Sciences USA 107(22): 10142-7

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 1-3

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

Ruiz-Trillo I., Roger A.J., Burger G., Gray M.W., and Lang B.F. (2008). A phylogenomic investigation into the origin of metazoa. Mol. Biol. Evol. 25, 664-672.

Bapteste E., Susko E., Leigh J., Ruiz-Trillo I., Bucknam J., and Doolittle W.F. (2008). Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol. Biol. Evol. 25, 83-91.

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.

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.

M. Adl S, 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.

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. Mol. Phylogenet. Evol. 33: 321- 332, 2004.

Iñaki Ruiz-Trillo, Jordi Paps, Mercè Loukota, Carles Ribera, Ulf Jondelius, Jaume Baguñà & Marta Riutort. (2002) A phylogenetic analysis of Myosin Heavy Chain type II sequences corroborates Acoela and Nemertodermatida are basal bilaterians. Proc. Natl. Acad. Sci. USA 99: 11246-11251.

Jondelius U, Iñaki Ruiz-Trillo, Jaume Baguñà & Marta Riutort. (2002) The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zoologica Scripta 31: 201-215.

Jaume Baguñà, Iñaki Ruiz-Trillo, Jordi Paps, Mercè Loukota, Carles Ribera, Ulf Jondelius & Marta Riutort. (2001) The first bilaterian organisms: simple or complex? New molecular evidence. Int. J. Dev. Biol. 45: S133-S134.

Iñaki Ruiz-Trillo, Marta Riutort, D. Timothy J. Littlewood, Elisabeth A. Herniou & Jaume Baguñà. (1999) Acoel flatworms: earliest extant bilaterian metazoans, not members of the Platyhelminthes. Science 283: 1919-1923. (*cover article)

Carranza S, Iñaki Ruiz-Trillo, D. Timothy J. Littlewood, Marta Riutort & Jaume Baguñà. (1998) A reappraisal of the phylogenetic and taxonomic position of land planarians (Platyhelminthes, Turbellaria, Tricladida) inferred from 18S rDNA sequences. Pedobiologia 42: 433-440.

Carranza S, D. T. J Littlewood, K. A. Clough, Ruiz-Trillo I, Baguñà J & Riutort M. (1998) A robust molecular phylogeny of the Tricladida (Platyhelminthes, Seriata) and a reassessment of morphological synapomorphies. Proc. R Soc. Lon. B 265: 631-640.


Book chapters

Barberà MJ, Ruiz-Trillo I, Jessica Leigh, Laura A. Hug & Andrew J. Roger. (2006) The diversity of mitochondrion-related organelles amongst eukaryotic microbes. In “Origins of Mitochondria and Hydrogenosomes”, Martin W. ed., Springer, Heidelberg (in press).

Ruiz-Trillo I (2001) Acoela. In “McGraw-Hill Encyclopedia of Science and Technology, 2001 Yearbook of Science & Technology”. McGraw-Hill, New York.

Baguñà J, Carranza S., Paps J, Ruiz-Trillo I & Riutort M. (2000) Molecular taxonomy and phylogeny of Tricladida. In “Interrelationships of the Platyhelminthes”, Littlewood & Bray Ed., Taylor & Francis, London.