Acels i nemertodermàtides: bilaterals basals o platihelmints? Aproximació multigénica a l'origen dels metazous bilaterals.

La transició d'animals amb un eix, simetria radial i dues capes embrionàries a animals amb dos eixos, simetria bilateral i tres capes embrionàries fou un dels esdeveniments més importants de la història evolutiva animal. Cóm eren els primers organismes bilaterals, els ancestres dels 34 fílums actuals de bilaterals, és un dels misteris més grans de la Zoologia i la Història Natural. Les dades morfològiques i paleontòlogiques han produit no poques teories de com es va donar aquest procés. En qualsevol cas, aquestes es poden simplificar en una pregunta: eren els primers bilaterals organismes estructuralment complexes (amb celoma, segmentació i amb estructures internes i nervioses desenvolupades) o bé morfològicament senzills? Les implicacions són evidents: si l'ancestre era complex, això implica que els bilaterals actuals d'organització corporal senzilla (els fílums acelomats i pseudocelomats) són derivats per simplificació. Si, d'altra banda, l'ancestre era estructuralment senzill, la complexitat corporal s'hauria adquirit gradualment. Entendre aquest pas ajudarà, entre d'altres coses, a: 1) polaritzar els canvis genètics i morfològics, 2) compendre les raons de l'augment o disminució de complexitat, i 3) iniciar estudis genètics en taxons clau per entendre la genètica subjacent de passar de un sol eix corporal (oral-aboral) a dos eixos corporals (antero-posterior i dorso-ventral).La condició sine qua non per respondre aquesta pregunta és disposar d'una filogènia robusta dels fílums animals. Així, adreçant-nos cap aquest objectiu, aquesta tesi ha intentat solventar la posició filogenètica de dos taxons: els acels i els nemertodermàtides. Avui en dia, la manera més eficaç d'afrontar això és obtenint dades independents de la morfologia; és a dir, obtenir dades moleculars i inferir-ne la seva posició filogenètica a partir d'aquestes. D'aquesta manera es pot testar i evaluar les teories proposades i, per què no?, generar hipòtesis noves. A l'inici de la tesi només disposavem de les seqüències del 18S de tres espècies d'acels i d'un nemertodermàtid, obtingudes per resoldre la situació del fílum Platyhelminthes (considerat basal fins aleshores) dins dels Bilateria. Els acels seqüenciats eren, però, fast-clock (presentaven tases de substitució més elevades que la resta). Davant d'aquest problema, l'aproximació molecular havia de seguir, doncs, unes pautes concretes, emprant diferents aproximacions i metodologies:1.seqüenciar més 18S d'acels i nemertodermàtides, per tal de trobar algun amb una taxa de substitució semblant a la resta de bilaterals. 2.buscar i trobar una molècula independent dels gens ribosomals, com, per exemple, gens nuclears codificants, amb informació filogenètica a nivell de fílums. Una vegada trobada seqüeincar un nombre suficientment alt de taxons per tal de comprobar els resultats del 18S. 3.obtenir dades sobre possibles sinapomorfies moleculars, com ara el nombre i tipus de gens Hox, el reordernament dels gens mitocondrials.Aquesta Tesi enfila el problema emprant moltes de les possibles aproximacions moleculars: a) generant més seqüències de 18S d'acels i nemertodermàtides (capítol I i II); b) aconseguint les primeres seqüències de proteïnes mitocondrials d'acels i nemertodermàtides (capítol II); c) cercant una nova molècula -gen codificant nuclear- amb informació filogenètica al nivell que volem i seqüenciant una serie suficient de fílums bilaterals per testar els resultats del 18S (capítol III); i d) generant les primeres dades dels genomes mitocondrials d'acels, nemertodermàtides i platihelmints no-paràsits, per tal de buscar sinapomorfies moleculars (capítol IV).Totes les dades aquí presentades (18S ribosomal, les sequencies del nou marcadaor filogenètic miosina II, i l'estructura dels genomes mitocondrials) corroboren que els Platyhelminthes són polifilètics, ja que ni acels ni nemertodermàtides s'agrupen amb el gruix dels Platyhelminthes (els Rhabditophora). De fet, el conjunt de dades presentades suggereixen un nou esquema taxonòmic i filogenètic dels Metazous: els Bilateria formen un grup monofilètic dividit en: 1) acels i nemertodermàtides i 2) el gruix dels bilaterals, que anomenem Eubilateria o Nephrozoa, dividits en els tres superclades (Ecdysozoa, Lophotrochozoa i Deuterostomia). Així, acels i nemertodermàtides haurien divergit abans que la resta dels bilaterals actuals, i seriens els bilaterals més basals de tots els actuals. La seva morfologia actual ens premetria, per tant, inferir que l'ancestre dels Bilateria era també morfològicament senzill, probablemenet sense celoma, sense segments i de desenvolupament directe

New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference

A report on the meeting Comparative Genomics of Eukaryotic Microorganisms: understanding the complexity of diversity. Sant Feliu de Guíxols, Spain. October 15-20, 2011

A genomic survey shows that the haloarchaeal type Tyrosyl-tRNA Synthetase is not a synapomorphy of opisthokonts

The haloarchaeal-type tyrosyl tRNA synthetase (tyrRS) have previously been proposed to be a molecular synapomorphy of the opisthokonts. To re-evaluate this we have performed a taxon-wide genomic survey of tyrRS in eukaryotes and prokaryotes. Our phylogenetic trees group eukaryotes with archaea, with all opisthokonts sharing the haloarchaeal-type tyrRS. However, this type of tyrRS is not exclusive to opisthokonts, since it also encoded by two amoebozoans. Whether this is a consequence of lateral gene transfer or lineage sorting remains unsolved, but in any case haloarchaeal-type tyrRS is not a synapomorphy of opisthokonts. This demonstrates that molecular markers should be re-evaluated once a better taxon sampling becomes available

Phylogenomic Evidence for a Myxococcal Contribution to the Mitochondrial Fatty Acid Beta-Oxidation

Background The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins. Methodology/Principal Findings Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid β-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer. Conclusions/Significance Our results support a prokaryotic origin, different from α-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to ente

Evolution of the MAGUK protein gene family in premetazoan lineages

<p>Abstract</p> <p>Background</p> <p>Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK) are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of <it>Capsaspora owczarzaki</it>, an unicellular organism that branches off near the metazoan clade. To further investigate the evolutionary history of MAGUK, we have undertook a broader search for this gene family using available genomic sequences of different opisthokont taxa.</p> <p>Results</p> <p>Our survey and phylogenetic analyses show that MAGUK proteins are present not only in Metazoa, but also in the choanoflagellate <it>Monosiga brevicollis </it>and in the protist <it>Capsaspora owczarzaki</it>. However, MAGUKs are absent from fungi, amoebozoans or any other eukaryote. The repertoire of MAGUKs in Placozoa and eumetazoan taxa (Cnidaria + Bilateria) is quite similar, except for one class that is missing in <it>Trichoplax</it>, while Porifera have a simpler MAGUK repertoire. However, Vertebrata have undergone several independent duplications and exhibit two exclusive MAGUK classes. Three different MAGUK types are found in both <it>M. brevicollis </it>and <it>C. owczarzaki: DLG, MPP and MAGI</it>. Furthermore, <it>M. brevicollis </it>has suffered a lineage-specific diversification.</p> <p>Conclusions</p> <p>The diversification of the MAGUK protein gene family occurred, most probably, prior to the divergence between Metazoa+choanoflagellates and the <it>Capsaspora</it>+<it>Ministeria </it>clade. A MAGI-like, a DLG-like, and a MPP-like ancestral genes were already present in the unicellular ancestor of Metazoa, and new gene members have been incorporated through metazoan evolution within two major periods, one before the sponge-eumetazoan split and another within the vertebrate lineage. Moreover, choanoflagellates have suffered an independent MAGUK diversification. This study highlights the importance of generating enough genome data from the broadest possible taxonomic sampling, in order to fully understand the evolutionary history of major protein gene families.</p

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

Opisthokonta represents a major lineage of eukaryotes and includes fungi and metazoans, as well as other less known unicellular groups. The latter are paraphyletic assemblages that branch in between the former two groups, and thus are important for understanding the origin and early diversification of opisthokonts. The full range of their diversity, however, has not yet been explored from diverse ecological habitats. Freshwater environments are crucial sources for new diversity; they are considered even more heterogeneous than marine ecosystems. This heterogeneity implies more ecological niches where local eukaryotic communities are located. However, knowledge of the unicellular opisthokont diversity is scarce from freshwater environments. Here, we performed an 18S rDNA metabarcoding study in the Middle Paraná River, Argentina, to characterize the molecular diversity of microbial eukaryotes, in particular unicellular members of Opisthokonta. We identified a potential novel clade branching as a sister-group to Fungi. We also detected in our data that more than 60% operational taxonomic units classified as unicellular holozoans (animals and relatives) represent new taxa at the species level. Of the remaining, the majority was assigned to the newly described holozoan species, Syssomonas multiformis. Together, our results show that a large hidden diversity of unicellular members of opisthokonts still remain to be uncovered. We also found that the geographical and ecological distribution of several taxa considered exclusive to marine environments is wider than previously thought

A Genomic Survey of HECT Ubiquitin Ligases in Eukaryotes Reveals Independent Expansions of the HECT System in Several Lineages

The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metazoans and plants. To have a wider perspective, here we perform a genomic survey of the HECT family of E3 ubiquitin-protein ligases, an important part of this posttranslational pathway, in genomes from representatives of all major eukaryotic lineages. We classify eukaryotic HECTs and reconstruct, by phylogenetic analysis, the putative repertoire of these proteins in the last eukaryotic common ancestor (LECA). Furthermore, we analyze the diversity and complexity of protein domain architectures of HECTs along the different extant eukaryotic lineages. Our data show that LECA had six different HECTs and that protein expansion and N-terminal domain diversification shaped HECT evolution. Our data reveal that the genomes of animals and unicellular holozoans considerably increased the molecular and functional diversity of their HECT system compared with other eukaryotes. Other eukaryotes, such as the Apusozoa Thecanomas trahens or the Heterokonta Phytophthora infestans, independently expanded their HECT repertoire. In contrast, plant, excavate, rhodophyte, chlorophyte, and fungal genomes have a more limited enzymatic repertoire. Our genomic survey and phylogenetic analysis clarifies the origin and evolution of different HECT families among eukaryotes and provides a useful phylogenetic framework for future evolutionary studies of this regulatory pathway

Earliest holozoan expansion of phosphotyrosine signaling

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.Phosphotyrosine (pTyr) signaling is involved in development and maintenance of metazoans' multicellular body through cell-to-cell communication. Tyrosine kinases (TKs), tyrosine phosphatases, and other proteins relaying the signal compose the cascade. Domain architectures of the pTyr signaling proteins are diverse in metazoans, reflecting their complex intercellular communication. Previous studies had shown that the metazoan-type TKs, as well as other pTyr signaling proteins, were already diversified in the common ancestor of metazoans, choanoflagellates, and filastereans (which are together included in the clade Holozoa) whereas they are absent in fungi and other nonholozoan lineages. However, the earliest-branching holozoans Ichthyosporea and Corallochytrea, as well as the two fungi-related amoebae Fonticula and Nuclearia, have not been studied. Here, we analyze the complete genome sequences of two ichthyosporeans and Fonticula, and RNAseq data of three additional ichthyosporeans, one corallochytrean, and Nuclearia. Both the ichthyosporean and corallochytrean genomes encode a large variety of receptor TKs (RTKs) and cytoplasmic TKs (CTKs), as well as other pTyr signaling components showing highly complex domain architectures. However, Nuclearia and Fonticula have no TK, and show much less diversity in other pTyr signaling components. The CTK repertoires of both Ichthyosporea and Corallochytrea are similar to those of Metazoa, Choanoflagellida, and Filasterea, but the RTK sets are totally different from each other. The complex pTyr signaling equipped with positive/negative feedback mechanism likely emerged already at an early stage of holozoan evolution, yet keeping a high evolutionary plasticity in extracellular signal reception until the co-option of the system for cell-to-cell communication in metazoans. © 2013 The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.This work was supported by the European Research Council Starting grant ERC-2007-StG-206883 to I.R.-T; Ministerio de Ciencia e Innovación grant BFU2008-02839/BMC to I.R.-T.; and the Marie Curie Intra-European Fellowship (MMEMA) within the 7th European Community Framework Programme to H.S.Peer Reviewe