References of "Baurain, Denis"
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See detailGenome sequencing of an endemic filamentous Antarctic cyanobacterium
Lara, Yannick ULg; Verlaine, Olivier ULg; Kleinteich, Julia et al

Poster (2015, August 03)

The strain Phormidium priestleyi ULC007 was isolated from a benthic mat located in a shallow freshwater pond in the Larsemann Hills (69°S), Western Antarctica. This strain belongs to a cyanobacterial ... [more ▼]

The strain Phormidium priestleyi ULC007 was isolated from a benthic mat located in a shallow freshwater pond in the Larsemann Hills (69°S), Western Antarctica. This strain belongs to a cyanobacterial cluster that appeared as potentially endemic (Taton et al. 2006). After obtaining an axenic isolate, we sequenced the genome of this strain in the frame of the BELSPO CCAMBIO project, in order to better understand the functioning, metabolism and adaptative strategies of cyanobacteria to the extreme Antarctic environment. [less ▲]

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See detailThe BCCM/ULC collection : a Biological Ressource Center for polar cyanobacteria
Wilmotte, Annick ULg; Renard, Marine ULg; Lara, Yannick ULg et al

Poster (2015, August 03)

In this study, during the 2013 MicroFun expedition, we sampled 72 locations around Svalbard including diverse biotopes such as glacial forefields, tundra soils, hot springs, soil crusts, microbial mats ... [more ▼]

In this study, during the 2013 MicroFun expedition, we sampled 72 locations around Svalbard including diverse biotopes such as glacial forefields, tundra soils, hot springs, soil crusts, microbial mats, wet walls, cryoconites, plankton and periphyton, in order to (1) assess the biodiversity of cyanobacteria around Svalbard, (2) verify the existence of biogeographical trends around the archipelago, and (3) compare these data with other polar (cold) areas, especially Antarctica. We used a pyrosequencing approach targeting cyanobacteria-specific 16S rRNA gene sequences to deeply study the cyanobacterial communities. [less ▲]

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See detailThe hidden face of the human macrophage chitotriosidase: taking a new look at this enzyme based on the biochemical and phylogenomic analysis of its chitin binding domain
Crasson, Oscar ULg; Legrand, François; Léonard, Raphaël ULg et al

Poster (2015, August)

Carbohydrates recognition is a critical process involved in numerous aspects of the cell biology such as inflammation, innate immune responses and proliferation. Chitin is an homopolysaccharide composed ... [more ▼]

Carbohydrates recognition is a critical process involved in numerous aspects of the cell biology such as inflammation, innate immune responses and proliferation. Chitin is an homopolysaccharide composed of β-1,4-linked N-acetylglucosamine (GlcNAc) units that is an abundant structural component of various infectious organisms like protozoans, nematodes and fungi. As there is no endogenous chitin produced by mammals, this polymer appeared to be a strategic target for innate immune agents which is why various carbohydrate binding proteins, associated or not with catalytic domains, are synthetized by plants and animals and are known to play a crucial role in innate immunity. The macrophage chitotriosidase (HCHT) is one of the three active chitinases synthetized by humans and has triggered significant attention recently due to its association with various inflammatory disorders. HCHT belongs to the Glycosyl Hydrolase family 18 (GH18) and is known to be involved in innate immunity. Nevertheless, its precise physiological function remains unclear. As numerous GHs, HCHT is a modular protein composed of a catalytic domain (GH18) associated to a Carbohydrate Binding Module (CBM) which is essential to hydrolyse crystalline chitin. If the catalytic domain GH18 is highly common in other GHs from animals, plants, fungi, bacteria, archea and viruses, its CBM (named ChBD) is much less conserved which makes the association between these two domains particularly intriguing. This work aims to demystify HCHT’s physiological function. Firstly, using competitive inhibition assays, we have highlighted the ability of ChBD to interact with chitooligosaccharides (GlcNAc1-2-4-6) which suggests that ChBD can potentially act as a lectin domain. Secondly, to better understand the molecular basis for chitin recognition, we have used homology modelling to build, with high confidence, the 3D structure model of ChBD. Based on this model, a specific set of residues has been selected for alanine scan mutagenesis which has allowed us to define the minimum chitin binding interface of the protein. Thirdly, Phylogenomic studies were performed to analyse the evolutionary history of the isolated catalytic and ChBD domains and understand how these domains were combined. Based on all these results, we discuss a new way of looking at HCHT where its ChBD would be the key determinant that has guided the catalytic domain from a basic metabolic function to a critical component of innate immunity in human. Finally, we propose a mechanism that explains how this enzyme could act at the molecular level to defend us against chitin-containing pathogens. [less ▲]

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See detailPinpointing the origin of plastids using phylogenomics
Baurain, Denis ULg

Scientific conference (2015, April 17)

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See detailRooting the tree of life: the phylogenetic jury is still out.
Gouy, Richard ULg; Baurain, Denis ULg; Philippe, Herve

in Philosophical transactions of the Royal Society of London. Series B, Biological sciences (2015), 370(1678), 20140329

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue ... [more ▼]

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework. [less ▲]

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See detailThe mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae.
Perez, Emilie ULg; Lapaille, Marie; Degand, Herve et al

in Mitochondrion (2014), 19 Pt B

The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential ... [more ▼]

The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential therapeutic target. Recently, numerous additional subunits of the respiratory-chain complexes have been described in Trypanosoma brucei and Trypanosoma cruzi. Since these subunits had apparently no counterparts in other organisms, they were interpreted as potentially associated with the parasitic trypanosome lifestyle. Here we used two complementary approaches to characterise the subunit composition of respiratory complexes in Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes. First, we developed a phylogenetic pipeline aimed at mining sequence databases for identifying homologs to known respiratory-complex subunits with high confidence. Second, we used MS/MS proteomics after two-dimensional separation of the respiratory complexes by Blue Native- and SDS-PAGE to both confirm in silico predictions and to identify further additional subunits. Altogether, we identified 41 subunits that are restricted to E. gracilis, T. brucei and T. cruzi, along with 48 classical subunits described in other eukaryotes (i.e. plants, mammals and fungi). This moreover demonstrates that at least half of the subunits recently reported in T. brucei and T. cruzi are actually not specific to Trypanosomatidae, but extend at least to other Euglenozoa, and that their origin and function are thus not specifically associated with the parasitic lifestyle. Furthermore, preliminary biochemical analyses suggest that some of these additional subunits underlie the peculiarities of the respiratory chain observed in Euglenozoa. [less ▲]

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See detailEvolution des eucaryotes : l'éclairage de la phylogénie moléculaire
Baurain, Denis ULg

Conference (2014, October 23)

Ce cours-conférence propose d'examiner l'origine et l'évolution des eucaryotes au travers de la biologie, la géologie et la paléontologie. Les eucaryotes forment un des trois domaines de la vie, et ... [more ▼]

Ce cours-conférence propose d'examiner l'origine et l'évolution des eucaryotes au travers de la biologie, la géologie et la paléontologie. Les eucaryotes forment un des trois domaines de la vie, et comprennent les animaux (dont les êtres humains), les plantes et les champignons, mais surtout une énorme majorité de protistes (eucaryotes unicellulaires) dont la diversité reste encore en partie à explorer. De grandes questions restent à élucider quant à l'origine du domaine Eucarya, sa position au sein de l'arbre de la vie, et les modalités et conditions de diversification et d'évolution depuis au moins 1,8 milliards d'années. La première leçon abordera l'origine de la cellule eucaryote, en discutant les différentes hypothèses existantes et la nature de LECA (Last Eucaryotic Common Ancestor). Comment tester ces hypothèses avec de nouvelles approches ? Comment révéler la diversité actuelle des eucaryotes encore en partie inexplorée et quelles réponses peut-elle apporter ? La seconde leçon présentera d'abord l'éclairage de la phylogénie moléculaire : comment utiliser les informations conservées dans le matériel génétique, pour mieux comprendre l'évolution des eucaryotes ? Quelles sont les possibilités et les limitations de la phylogénomique et des horloges moléculaires ? On présentera ensuite les informations enregistrées dans le registre fossile du Précambrien. Comment reconnaitre les eucaryotes fossiles, les étudier, et reconstruire leur évolution et diversification dans les conditions paléoenvironnementales depuis au moins 1,8 milliards d'années ? Ces deux leçons donneront donc un aperçu de l'état des connaissances, des nouvelles méthodes utilisées, et des grandes énigmes à résoudre à propos de notre domaine Eucarya. [less ▲]

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See detailUnveiling biogeographic patterns of Antarctic cyanobacteria by 454 pyrosequencing
Wilmotte, Annick ULg; Stelmach Pessi, Igor ULg; De Carvalho, Pedro et al

Poster (2014, August)

Cyanobacteria are often considered as the dominant phototrophs in Antarctic lacustrine environments, primarily occurring in benthic or floating microbial mat communities. Previous studies have indicated ... [more ▼]

Cyanobacteria are often considered as the dominant phototrophs in Antarctic lacustrine environments, primarily occurring in benthic or floating microbial mat communities. Previous studies have indicated the presence of endemic cyanobacteria in the Antarctic Realm, but the extent and patterns of cyanobacterial bioregionalisation, if any, is still largely unknown. Therefore, our objective is to assess the cyanobacterial diversity in Antarctic lacustrine microbial mats using 454 pyrosequencing, in order to determine if cyanobacterial biogeographic patterns are similar to those observed for multicellular organisms. This will be useful also as baseline data, for later comparisons and assessments of the impact of global change. [less ▲]

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See detailTranscriptomics and Proteomics of a Secondary Green Alga.
Perez, Emilie ULg; Lapaille, Marie; Degand, Hervé et al

Poster (2014, August)

Euglena gracilis is a secondary green alga related to trypanosomes that derives from a secondary endosymbiosis between a phagotrophic ancestor and a prasinophycean green alga. Our general objective is to ... [more ▼]

Euglena gracilis is a secondary green alga related to trypanosomes that derives from a secondary endosymbiosis between a phagotrophic ancestor and a prasinophycean green alga. Our general objective is to study the metabolic interactions established between the secondary plastid and the mitochondrion after the endosymbiotic event and to determine the phylogenetic origin of the genes encoding the proteins involved in the energetic pathways. As a first step, we analysed the subunit composition of the mitochondrial respiratory chain, both in silico and by targeted proteomics, to assess the extent of its similitude with the respiratory chain of Trypanosomatidae. We have shown that Euglena shares many additional subunits with trypanosomes, which suggests that these subunits are not especially associated to a parasitic lifestyle. As a second step, we sequenced the total transcriptome of Euglena and determined the phylogenetic origin of each predicted transcript using a database of about 1000 complete proteomes representing the diversity of life. These analyses confirmed that Euglena recruited its genes from a very diverse set of sources. As a third step, we performed a high-throughput analysis of the mitochondrial proteome of Euglena. Our MS/MS experiments, taking advantage of the availability of our transcriptome, mostly recovered mitochondrial proteins, which indicates that our mitochondrial extracts were quite pure. The identified proteins encompassed about 15 different mitochondrial pathways. We are now in the process of comparing the expression levels of both the transcripts and the corresponding proteins across a range of culture conditions selected to differently stimulate the mitochondrion and the plastid. [less ▲]

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See detailHigh throughput sequencing analysis reveals genetic variability and selection pressure in different murine norovirus genomic regions during in vitro replication
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Poster (2014, July)

Murine norovirus (MuNoV), a single stranded positive sense RNA virus belonging to the Caliciviridae family, is considered as a representative model for human norovirus infections, one of the most ... [more ▼]

Murine norovirus (MuNoV), a single stranded positive sense RNA virus belonging to the Caliciviridae family, is considered as a representative model for human norovirus infections, one of the most important etiological cause of both epidemic and sporadic gastroenteritis cases worldwide. Four open reading frames are described into its genome: ORF1 codes the non-structural (NS) proteins, including the viral RNA dependent RNA polymerase (RdRp); ORF2 codes the single capsid protein (VP1), wherein two domains are present: a relatively conserved domain (“shell”) and a more variable domain (“protruding”); ORF3 codes a minor structural protein; and ORF4, currently only found in viruses genetically related to MuNoV codes a virulence factor. In this study, we demonstrated by high throughput sequencing that, during serial passages of MuNoV in cell culture, the substitution rates, estimated by Bayesian inferences, did not significantly differ across the five targeted genomic regions except one. These rates were similar in four genomic regions encompassing partial non-structural 1-2 protein (NS1-2)-, NS5-, NS6-, NS7 (RdRp)- and VP1-coding sequences (coding the conserved part of the protein also including the ORF4 region). In the partial minor structural protein-coding region, this substitution rate was however estimated to be at least one log higher when expressed as substitution/site/day. The precise localisation of the detected nucleotide point mutations (substitution, deletion and insertion) were reported as well as the quantitative increase or decrease of the sequences harbouring them along ten cell culture passages. The non-silent amino acid mutations were also depicted in 3D models for four out of the five studied regions. These results have important implications for different norovirus research fields, especially in terms of diagnosis, classification methodology and genetic evolution. [less ▲]

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See detailA Phylogenomic analysis of the origin of plastids
Cornet, Luc ULg; Javaux, Emmanuelle ULg; Wilmotte, Annick ULg et al

Conference (2014, June 24)

Cyanobacteria are a morphologically diverse phylum, with their first occurrence dating from the Precambrian. Oxygenic photosynthesis appeared in this group during the same geological period. Several ... [more ▼]

Cyanobacteria are a morphologically diverse phylum, with their first occurrence dating from the Precambrian. Oxygenic photosynthesis appeared in this group during the same geological period. Several publications have established, without any doubt, that plastids (both primary and complex) form a monophyletic ensemble emerging from Cyanobacteria. However, the exact position of plastids within Cyanobacteria is still uncertain, with several recent papers leading to very different hypotheses. Here we present a phylogenomic analysis of the origin of plastids. Our study takes advantage of all the available genomes and thus represents the best taxonomic sampling seen so far: 140 genomes of Cyanobacteria, 101 genomes of plastids and 27 outgroups taken in Melainabacteria and Chloroflexi. It results in an analysis using state-of-the-art methods (e.g., orthology assessment using USEARCH and OrthoMCL, phylogenetic inference using CAT and CAT-GTR models) based on more than 160 protein alignments totalizing over 20,000 unambiguously aligned amino acids. To confirm our results, we performed gene jackknife inferences and gene reconciliation analyses on the same dataset. We expect that out approach accounts for potential phylogenetic artefacts due to changes in the evolutionary process having occurred when the guest cyanobacterium became an endosymbiont and eventually a plastid. Meanwhile, we improve the phylogeny of Cyanobacteria per se, notably because of the presence of Melainabacteria in our dataset. [less ▲]

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See detailMitochondrial Proteomics of a Secondary Green Alga.
Perez, Emilie ULg; Degand, Hervé; Morsomme, Pierre et al

Poster (2014, May 06)

Euglena gracilis is an alga that derives from a secondary endosymbiosis with a green alga. Our general objective is to study the interactions established between the chloroplast and the mitochondrion ... [more ▼]

Euglena gracilis is an alga that derives from a secondary endosymbiosis with a green alga. Our general objective is to study the interactions established between the chloroplast and the mitochondrion during the endosymbiosic event and to determine the phylogenetic origin of the genes encoding the proteins involved in these interactions. As a first step, we performed a high-throughput analysis of the mitochondrial proteome of Euglena gracilis. Our MS/MS experiments mostly recover mitochondrial proteins representing 15 mitochondrial pathways, which indicates that our mitochondrial extracts are relatively pure, but the phylogenetic origins of the corresponding genes are surprisingly diverse. [less ▲]

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See detailL'analyse par séquençage à haut débit révèle la variabilité génétique et la pression de sélection dans différentes régions génomiques du norovirus murin durant sa réplication in vitro
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Conference (2014, March)

Le norovirus murin (MuNoV), un virus à ARN de polarité positive appartenant à la famille des Caliciviridae, est considéré comme un modèle adéquat pour les infections humaines à norovirus, une des causes ... [more ▼]

Le norovirus murin (MuNoV), un virus à ARN de polarité positive appartenant à la famille des Caliciviridae, est considéré comme un modèle adéquat pour les infections humaines à norovirus, une des causes étiologiques les plus importantes dans les cas de gastroentérite épidémique ou sporadique dans le monde entier. Quatre cadres de lecture ouverts (ORF) sont décrits au sein de son génome : l’ORF1 code les protéine non structurales (NS), dont l’ARN polymérase ARN dépendante virale (RdRp) ; l’ORF2 code l’unique protéine de capside (VP1), dans laquelle sont décrites deux régions : une relativement conservée (domaine « shell ») et une autre beaucoup plus variable (domaine « protruding ») ; l’ORF3 code une protéine structurale mineure ; et l’ORF4, actuellement uniquement décrit chez les virus génétiquement apparentés au MuNoV, code un facteur de virulence. Dans cette étude, nous démontrons par séquençage à haut débit que, durant des passages successifs du MuNoV en culture cellulaire, les taux de substitution, estimés par inférences Bayésiennes, n’ont pas significativement différé au travers des cinq régions génomiques ciblées à l’exception d’une région bien précise. Ces taux étaient similaires pour quatre régions englobant des séquences partielles codant les protéines non structurales NS1-2, NS5, NS6 et NS7 (RdRp) et VP1 dans sa région conservée (incluant également l’ORF4). Dans la région codant partiellement la protéine structurale mineure, ce taux de substitution, exprimé en substitution/site/jour, a été cependant estimé être plus élevée d’au moins une unité logarithmique. La localisation précise des mutations ponctuelles détectées (substitution, délétion et insertion) est rapportée ainsi que l’augmentation ou la diminution quantitative du nombre des séquences qui les présentaient au cours de dix passages successifs en culture cellulaire. Les localisations des mutations non silencieuses ont aussi été représentées dans une modélisation tridimensionnelle de quatre des cinq régions étudiées. Ces résultats ont d’importantes implications pour différents champs de recherche sur les norovirus, spécialement en termes de diagnostic, de méthodologie de classification et d’évolution génétique. [less ▲]

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See detailChromera velia, Endosymbioses and the Rhodoplex Hypothesis - Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles and Haptophytes (CASH Lineages)
Petersen, Jörn; Ludewig, Ann-Kathrin; Michael, Victoria et al

in Genome Biology and Evolution (2014), 6(3), 666-684

The discovery of Chromera velia, a free-living photosynthetic relative of apicomplexan pathogens, has provided an unexpected opportunity to study the algal ancestry of malaria parasites. In this work we ... [more ▼]

The discovery of Chromera velia, a free-living photosynthetic relative of apicomplexan pathogens, has provided an unexpected opportunity to study the algal ancestry of malaria parasites. In this work we compared the molecular footprints of a eukaryote-to-eukaryote endosymbiosis in C. velia to their equivalents in peridinin-containing dinoflagellates (PCD) to re- evaluate recent claims in favor of a common ancestry of their plastids. To this end, we established the draft genome and a set of full-length cDNA sequences from C. velia via next- generation sequencing. We documented the presence of a single coxI gene in the mitochondrial genome, which thus represents the genetically most reduced aerobic organelle identified so far, but focused our analyses on five “lucky genes” of the Calvin cycle. These were selected because of their known support for a common origin of complex plastids from cryptophytes, alveolates (represented by PCDs), stramenopiles and haptophytes (CASH) via a single secondary endosymbiosis with a red alga. As expected, our broadly sampled phylogenies of the nuclear- encoded Calvin cycle markers support a rhodophycean origin for the complex plastid of Chromera. However, they also suggest an independent origin of apicomplexan and dinophycean (PCD) plastids via two eukaryote-to-eukaryote endosymbioses. Although at odds with the current view of a common photosynthetic ancestry for alveolates, this conclusion is nonetheless in line with the deviant plastome architecture in dinoflagellates and the morphological paradox of four versus three plastid membranes in the respective lineages. Further support for independent endosymbioses is provided by analysis of five additional markers, four of them involved in the plastid protein import machinery. Finally, we introduce the “rhodoplex hypothesis” as a convenient way to designate evolutionary scenarios where CASH plastids are ultimately the product of a single secondary endosymbiosis with a red alga, but were subsequently horizontally spread via higher-order eukaryote-to-eukaryote endosymbioses. [less ▲]

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See detailOrigin and evolution of metal P-type ATPases in Plantae (Archaeplastida)
Hanikenne, Marc ULg; Baurain, Denis ULg

in Frontiers in Plant Science (2014), 4

Metal ATPases are a subfamily of P-type ATPases involved in the transport of metal cations across biological membranes. They all share an architecture featuring eight transmembrane domains in pairs of two ... [more ▼]

Metal ATPases are a subfamily of P-type ATPases involved in the transport of metal cations across biological membranes. They all share an architecture featuring eight transmembrane domains in pairs of two and are found in prokaryotes as well as in a variety of Eukaryotes. In Arabidopsis thaliana, eight metal P-type ATPases have been described, four being specific to copper transport and four displaying a broader metal specificity, including zinc, cadmium and possibly copper and calcium. So far, few efforts have been devoted to elucidating the origin and evolution of these proteins in Eukaryotes. In this work, we use large-scale phylogenetics to show that metal P-type ATPases form a homogenous group among P-type ATPases and that their specialisation into either monovalent (Cu) or divalent (Zn, Cd…) metal transport stems from a gene duplication that took place early in the evolution of Life. Then, we demonstrate that the four subgroups of plant metal ATPases all have a different evolutionary origin and a specific taxonomic distribution, only one tracing back to the cyanobacterial progenitor of the chloroplast. Finally, we examine the subsequent evolution of these proteins in green plants and conclude that the genes thoroughly characterised in model organisms are often the result of lineage-specific gene duplications, which calls for caution when attempting to infer function from sequence similarity alone in non-model organisms. [less ▲]

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See detailIdentifying losses and expansions of selected gene families in incomplete genomic datasets
Di Franco, Arnaud ULg; Hanikenne, Marc ULg; Baurain, Denis ULg

Poster (2013, December 09)

Plantae (Archaeplastida) are a natural group of organisms with plastids of primary endosymbiotic origin. Within this group, members of the red algae show evidence of a reduction of their genomic content ... [more ▼]

Plantae (Archaeplastida) are a natural group of organisms with plastids of primary endosymbiotic origin. Within this group, members of the red algae show evidence of a reduction of their genomic content. In this work, we designed a bioinformatics approach to investigate the few, sometimes incomplete, genomic datasets available for red algae, with the purpose of pointing out possible gene family losses and expansions. Our pipeline first populates a relational database with precomputed orthology relationships between green plant genomes and red algal datasets and then efficiently queries the database for computing statistics of losses and expansions for a series of gene families of interest. [less ▲]

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See detailAssessment of bioinformatic pipelines for the analysis of 454 pyrosequencing data using artificial cyanobacterial communities
Stelmach Pessi, Igor ULg; de Carvalho Maalouf, Pedro; Laughinghouse IV, Haywood Dail et al

Poster (2013, November)

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See detailComputers As Genomic Time Machines for Meeting our Ancestors
Baurain, Denis ULg

Scientific conference (2013, April 18)

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See detailImpact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
Roure, Béatrice; Baurain, Denis ULg; Philippe, Hervé

in Molecular Biology and Evolution (2013), 30(1), 197-214

Progress in sequencing technology allows researchers to assemble ever-larger supermatrices for phylogenomic inference. However, current phylogenomic studies often rest on patchy data sets, with some ... [more ▼]

Progress in sequencing technology allows researchers to assemble ever-larger supermatrices for phylogenomic inference. However, current phylogenomic studies often rest on patchy data sets, with some having 80% missing (or ambiguous) data or more. Though early simulations had suggested that missing data per se do not harm phylogenetic inference when using sufficiently large data sets, Lemmon et al. (Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 58:130-145.) have recently cast doubt on this consensus in a study based on the introduction of parsimony-uninformative incomplete characters. In this work, we empirically reassess the issue of missing data in phylogenomics while exploring possible interactions with the model of sequence evolution. First, we note that parsimony-uninformative incomplete characters are actually informative in a probabilistic framework. A reanalysis of Lemmon's data set with this in mind gives a very different interpretation of their results and shows that some of their conclusions may be unfounded. Second, we investigate the effect of the progressive introduction of missing data in a complete supermatrix (126 genes × 39 species) capable of resolving animal relationships. These analyses demonstrate that missing data perturb phylogenetic inference slightly beyond the expected decrease in resolving power. In particular, they exacerbate systematic errors by reducing the number of species effectively available for the detection of multiple substitutions. Consequently, large sparse supermatrices are more sensitive to phylogenetic artifacts than smaller but less incomplete data sets, which argue for experimental designs aimed at collecting a modest number (∼50) of highly covered genes. Our results further confirm that including incomplete yet short-branch taxa (i.e., slowly evolving species or close outgroups) can help to eschew artifacts, as predicted by simulations. Finally, it appears that selecting an adequate model of sequence evolution (e.g., the site-heterogeneous CAT model instead of the site-homogeneous WAG model) is more beneficial to phylogenetic accuracy than reducing the level of missing data. [less ▲]

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See detailThe unusual Gasteromycetes Lycogalopsis solmsii belongs to the gomphoid-phalloid group
Demoulin, Vincent ULg; Cornet, Luc ULg; Delbruyère, Emilie et al

in Acta Mycologica (2013), 48(1), 13-20

The rare tropical Gasteromycetes Lycogalopsis solmsii has been found twice at thirty years interval in the Singapore Botanic Gardens. From the most recent find a culture could be isolated, which allowed ... [more ▼]

The rare tropical Gasteromycetes Lycogalopsis solmsii has been found twice at thirty years interval in the Singapore Botanic Gardens. From the most recent find a culture could be isolated, which allowed DNA extraction and sequencing of about 2000 bp from the nuclear ribosomal DNA. Comparison to a large sample of Basidiomycetes was only possible for a part of the large ribosomal subunit, but clearly indicated affiliation to the gomphoid-phalloid group, without any relationship to Lycoperdales or Agaricales, as stated in the Dictionary of the Fungi. [less ▲]

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