Tesi: "Lateral gene transfers"

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Vieira, Rute Gomes Velosa. "Bayesian phylogenetic modelling of lateral gene transfers". Thesis, University of Newcastle upon Tyne, 2015. http://hdl.handle.net/10443/3018.

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Phylogenetic trees represent the evolutionary relationships between a set of species. Inferring these trees from data is particularly challenging sometimes since the transfer of genetic material can occur not only from parents to their o spring but also between organisms via lateral gene transfers (LGTs). Thus, the presence of LGTs means that genes in a genome can each have di erent evolutionary histories, represented by di erent gene trees. A few statistical approaches have been introduced to explore non-vertical evolution through collections of Markov-dependent gene trees. In 2005 Suchard described a Bayesian hierarchical model for joint inference of gene trees and an underlying species tree, where a layer in the model linked gene trees to the species tree via a sequence of unknown lateral gene transfers. In his model LGT was modeled via a random walk in the tree space derived from the subtree prune and regraft (SPR) operator on unrooted trees. However, the use of SPR moves to represent LGT in an unrooted tree is problematic, since the transference of DNA between two organisms implies the contemporaneity of both organisms and therefore it can allow unrealistic LGTs. This thesis describes a related hierarchical Bayesian phylogenetic model for reconstructing phylogenetic trees which imposes a temporal constraint on LGTs, namely that they can only occur between species which exist concurrently. This is achieved by taking into account possible time orderings of divergence events in trees, without explicitly modelling divergence times. An extended version of the SPR operator is introduced as a more adequate mechanism to represent the LGT e ect in a tree. The extended SPR operation respects the time ordering. It additionaly di ers from regular SPR as it maintains a 1-to-1 correspondence between points on the species tree and points on each gene tree. Each point on a gene tree represents the existence of a population containing that gene at some point in time. Hierarchical phylogenetic models were used in the reconstruction of each gene tree from its corresponding gene alignment, enabling the pooling of information across genes. In addition to Suchard's approach, we assume variation in the rate of evolution between di erent sites. The species tree is assumed to be xed. A Markov Chain Monte Carlo (MCMC) algorithm was developed to t the model in a Bayesian framework. A novel MCMC proposal mechanism for jointly proposing the gene tree topology and branch lengths, LGT distance and LGT history has been developed as well as a novel graphical tool to represent LGT history, the LGT Biplot. Our model was applied to simulated and experimental datasets. More speci cally we analysed LGT/reassortment presence in the evolution of 2009 Swine-Origin In uenza Type A virus. Future improvements of our model and algorithm should include joint inference of the species tree, improving the computational e ciency of the MCMC algorithm and better consideration of other factors that can cause discordance of gene trees and species trees such as gene loss.

2

Tofigh, Ali. "Using Trees to Capture Reticulate Evolution : Lateral Gene Transfers and Cancer Progression". Doctoral thesis, KTH, Beräkningsbiologi, CB, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-10608.

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The historic relationship of species and genes are traditionally depicted using trees. However, not all evolutionary histories are adequately captured by bifurcating processes and an increasing amount of research is devoted towards using networks or network-like structures to capture evolutionary history. Lateral gene transfer (LGT) is a previously controversial mechanism responsible for non tree-like evolutionary histories, and is today accepted as a major force of evolution, particularly in the prokaryotic domain. In this thesis, we present models of gene evolution incorporating both LGTs and duplications, together with efficient computational methods for various inference problems. Specifically, we define a biologically sound combinatorial model for reconciliation of species and gene trees that facilitates simultaneous consideration of duplications and LGTs. We prove that finding most parsimonious reconciliations is NP-hard, but that the problem can be solved efficiently if reconciliations are not required to be acyclic—a condition that is satisfied when analyzing most real-world datasets. We also provide a polynomial-time algorithm for parametric tree reconciliation, a problem analogous to parametric sequence alignment, that enables us to study the entire space of optimal reconciliations under all possible cost schemes. Going beyond combinatorial models, we define the first probabilistic model of gene evolution incorporating a birth-death process generating duplications, LGTs, and losses, together with a relaxed molecular clock model of sequence evolution. Algorithms based on Markov chain Monte Carlo (MCMC) techniques, methods from numerical analysis, and dynamic programming are presented for various probability and parameter inference problems. Finally, we develop methods for analysis of cancer progression, a biological process with many similarities to the process of evolution. Cancer progresses by accumulation of harmful genetic aberrations whose patterns of emergence are graph-like. We develop a model of cancer progression based on trees, and mixtures thereof, that admits an efficient structural EM algorithm for finding Maximum Likelihood (ML) solutions from available cross-sectional data.
QC 20100812

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Belliardo, Carole. "Étude des transferts horizontaux de gènes chez les nématodes phytoparasites par l'exploitation de métagénomes du sol". Electronic Thesis or Diss., Université Côte d'Azur, 2022. http://theses.univ-cotedazur.fr/2022COAZ6032.

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Les nématodes phytoparasites (NPP) sont parmi les plus importants ravageurs des cultures et menacent l'approvisionnement alimentaire mondial. Outre la nécessité de comprendre leur biologie pour développer de nouvelles stratégies de lutte, ces organismes sont fascinants en termes d'évolution génomique. Le parasitisme des plantes a évolué plusieurs fois indépendamment chez les nématodes selon des processus évolutifs convergents. Il semble que tous les NPP aient acquis des gènes bactériens et fongiques par transferts horizontaux de gènes (THG). Certains des gènes acquis horizontalement sont impliqués dans des fonctions parasitaires essentielles comme la dégradation des parois cellulaires des plantes ou l'assimilation des nutriments provenant des plantes. Cependant, plusieurs questions majeures restent encore en suspens concernant l'origine de ces gènes, leur distribution dans les génomes et la chronologie des événements d'acquisition. La plupart des NPP vivent dans le sol; nous pouvons donc supposer que ces gènes proviennent des micro-organismes du sol. Cependant, la sous-représentation de ces micro-organismes dans les librairies de séquences généralistes a probablement limité les précédentes analyses sur les THG. Pour pallier ce problème, nous avons constitué une bibliothèque de protéines provenant de plus de 6 800 métagénomes du sol disponibles publiquement. Un problème important dans les données métagénomiques concerne la qualité des données provenant des organismes eucaryotes due à l'utilisation d'outils dédiés aux génomes procaryotes. Afin de mieux représenter le pool de gènes présents dans les environnements naturels des NPP, nous avons identifié les contigs eucaryotes et re-prédit les gènes et protéines en utilisant un prédicteur de gènes eucaryotes.. Nous avons, ainsi, obtenu une librairie de protéines fiable et non redondante plus représentative de la biodiversité naturelle du sol.En utilisant cette librairie enrichie en protéines de sol, nous avons effectué une détection de THG sur 18 génomes de NPP du clade Tylenchina constituant un groupe très diversifié de modes de parasitisme. Après curation manuelle, la proportion de gènes acquis par transferts horizontaux avec confirmation phylogénétique est comprise entre 0.5 et 1,9% des gènes codant pour des protéines. Les THG dans les génomes de NPP proviennent principalement de bactéries. Nous avons également observé des THG provenant d'organismes eucaryotes tels que des champignons et pour la première fois des protistes et des plantes. Les taxa les plus représentés parmi les donneurs sont des espèces vivant dans le sol des clades bactériens Burkholderiaceae, Proteobacteria, Actinobacteria, Rhizobiales et fongiques (Dikary)a. L'utilisation de données métagénomiques a permis de préciser l'histoire des THG déjà décrits mais aussi d'identifier des centaines de nouveaux THG. Les prédictions fonctionnelles des THG nouvellement identifiées indiquent une large diversité de fonctions potentielles dont les implications biologiques pourront être plus précisément décrites dans le cadre d'expériences biochimiques. L'intégration de données environnementales dans notre librairie de référence a permis d'étendre la détection des THG et de compléter le catalogue des descendants des potentiels donneurs
Plant-parasitic nematodes (PPN) are among the most important crop pests and threaten the world's food production. Besides the need to understand their biology to develop new control strategies, they are fascinating organisms in terms of genomic evolution. Plant parasitism has evolved several times independently in nematodes with some convergent evolutionary processes. For instance, all studied PPN have acquired bacterial and fungal genes by horizontal gene transfers (HGT). Some of the acquired genes are involved in essential parasitic functions like plant cell wall degradation or processing nutrients from the plant. However, several major questions concerning their origin, evolutionary fate and distribution in the genomes and timing of acquisition events remain unsolved. Most PPN live in soil; thus, we hypothesised that these genes originated from soil-dwelling microorganisms. However, the underrepresentation of soil microorganisms in generalist sequence libraries has previously limited HGT analyses.To circumvent this problem, we built a protein library including more than 6,800 soil metagenomes from the Joint Genome Institute's IMG/M server. The first challenge was to make this massive dataset more accurate and suitable for HGT analysis in PPN genomes. An important issue in metagenomic data is the underrepresentation of eukaryotes and their annotation with prokaryotic tools. To better represent the pool of genes present in the natural environments of PPN, we identified eukaryotic contigs and re-predicted proteins using Augustus, a eukaryotic dedicated gene predictor. Moreover, we reduced the protein sequence redundancy and refined the taxonomic assignment. After all these steps, we obtained an improved and non-redundant database that was more representative of the soil's natural biodiversity. This soil protein library, two times larger than the classic library, contains mainly organisms genetically divergent than lab-cultured.Then, we performed an HGT detection on proteins from 18 plant-parasitic nematode genomes of the Tylenchina clade, constituting a highly diverse group of PPN phenotypes, against our library enriched with soil protein. After manual curation, the proportion of genes acquired by horizontal transfers with phylogenetic confirmation is between 0.5 to 1.9% to protein-coding genes originating from HGT in PPN genomes. Those genes mainly originate from bacteria, but we also observed HGT from eukaryotic kingdoms such as fungi, protists and plants. The most represented taxa in donors are soil-dwelling species of clades Burkholderiaceae, Proteobacteria, Actinobacteria, Rhizobiales and Dikarya. The usage of metagenomic data clarified the history of previously described HGTs but also identified hundreds of new HGTs. Functional analyses of the newly identified HGTs indicate a wide diversity of potential functions whose biological implications can be more precisely described in in-vitro experiments. Integrating environmental data in our reference library has allowed us to extend the detection of HGTs and to complete the catalog of potential donor offspring

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Lester, Leo. "On Lateral Gene Transfer". Thesis, University of Reading, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487489.

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Is bacterial evolution phylogenetic or reticulate? Darwin showed that life's history W;J.S mappable with trees. For almost everytfillg that we can see about us, this is largely correct, but beyond the limit of our sight thrives the unseen majority: The tiny, singlecelled prokaryotes do not reserve their genes only for the next generation. Through lateral gene transfer they swap genes with contemporaries, regardless of species. Discovered in the war years, the true place of lateral gene transfer within evolution has not yet been settled. As work on it.has multiplied, so its apparent extent has grown. Here a reappraisal of lateral gene transfer is carried out. The methods of its detection are examined and refined. The ~sults show that lateral transfer is not nearly so prevalent as some say. Less frequent, but still important, lateral gene transfer is shown to be a key mover in the evolution of the entire eukaryote domain. Its effect on individual genes, how it can increase rates of evolution and even trigger 'positive selection regimes, is exposed. The interconnectivity of species is then explored. Species that are the source of many genes receive many. Species that receive lots of genes through lateral transfer hold fewer unique genes. In addition, it is as if all species are connected through a massive network of lateral transfers. But any new information must be placed in its proper context: lateral gene transfer is only one of evolution's tools. Convergent evolution is exposed as a problem, both when trying to detect lateral transfer and perhaps also when constructing phylogenies. For all our problems with bacterial phylogenies, with building and interpreting them, the lesson of lateral gene transfer is that we can have faith in the idea of bacterial species and, after almost a hundred and fifty years, in Darwin too.

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Cheeseman, Kevin. "Aspects of Penicillium genomics : Molecular combing genome assembly, genetic exchange in food and potential for secondary metabolite production". Thesis, Paris 11, 2013. http://www.theses.fr/2013PA112280/document.

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Les Penicilliums sont des champignons filamenteux appartenant au genre Ascomycota. Ces champignons ont été utilisés par l’homme pour la production de nourriture depuis des siècles. Plus récemment, ils ont aussi été utilisés dans l’industrie biotechnologique pour la production de composés chimiques d’intérêts pharmaceutiques. Certaines espèces de Penicillium sont par ailleurs des moisissures contaminants certains aliments, d’autres sont des pathogènes de plantes, y compris de certains fruits. Leur génomique est globalement peut connue. Dans cette étude, nous avons analysé les génomes de deux espèces nouvellement séquencées, Penicillium roqueforti et Penicillium camemberti. Nous reportons ici le développement d’une nouvelle méthodologie pour l’amélioration et la validation d’assemblage de génomes en utilisant une technologie permettant l’observation de molécules d’ADN unique, le Peignage Moléculaire. En utilisant cette méthode, nous avons amélioré l’assemblage de Penicillium roqueforti. Ce manuscrit décrit aussi de multiples occurrences d’un transfert horizontal d’un ilot génomique de plus de cinq cent kilobases entre plusieurs Penicillium. Ce cas de transfert horizontal indique une fréquence d’échange latéral de matériel génétique plus forte qu’attendue. Enfin nous présentons un inventaire préliminaire du potentiel génomique pour la production de métabolites secondaires dans ces importants Penicillium alimentaires
Penicillium are filamentous fungi belonging to the Ascomycota genus. Penicillium species have been used by Man for centuries in food making processes. More recently they have also been used in the biotechnology industry for the production of compounds of pharmaceutical interest. Some Penicillium species are food spoilage agents, pathogens of plants including fruits. Aspects of their genomics are largely unknown. In this study, we analysed the genomes of two newly sequenced species, Penicillium roqueforti and Penicillium camemberti. Here we report the development of a new methodology for improving and validating genome assembly using an original single DNA molecule technology, Molecular Combing. Using this methodology we were able to produce a high quality genome assembly of Penicillium roqueforti. This work also reports the multiple and recurrent horizontal transfer of a large genomic island of over half a megabase between several Penicillium species. This horizontal transfer indicates a higher frequency of lateral genetic exchange between cheesemaking fungi than previously expected. Finally, we present an early assessment of the genomic potential for secondary metabolite production in these important food associated penicilliums

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Addario-Berry, Dana. "An analysis of models and algorithms for gene duplication and lateral gene transfer /". Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80161.

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The construction of phylogenetic trees commonly uses molecular sequence data (DNA, RNA or amino acid sequences) for a single gene family over a set of n extant taxa. However, difficulties arise when the phylogenetic gene tree for one gene family disagrees with the phylogenetic gene tree for a different gene family. Several computational problems arise when trying to explain this disagreement (the two gene trees are not equal). Typically, one assumes a (simplified) model of evolution restricted to a small set of events which are assumed to cause the disagreement. Two such well-studied events are gene duplications and lateral gene transfer (a.k.a. horizontal gene transfer).
This thesis explores several aspects of both of these simplifed models of evolution. A brief exposition of the models is presented, along with previous results and various extensions to these models.
The expected number of gene duplications needed to explain disagreements between a random gene and species tree is investigated.
A method for incorporating edge weights into the species tree is proposed.

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Khan, Mehmood Alam. "Computational Problems in Modeling Evolution and Inferring Gene Families". Doctoral thesis, KTH, Beräkningsvetenskap och beräkningsteknik (CST), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-193637.

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Over the last few decades, phylogenetics has emerged as a very promising field, facilitating a comparative framework to explain the genetic relationships among all the living organisms on earth. These genetic relationships are typically represented by a bifurcating phylogenetic tree — the tree of life. Reconstructing a phylogenetic tree is one of the central tasks in evolutionary biology. The different evolutionary processes, such as gene duplications, gene losses, speciation, and lateral gene transfer events, make the phylogeny reconstruction task more difficult. However, with the rapid developments in sequencing technologies and availability of genome-scale sequencing data, give us the opportunity to understand these evolutionary processes in a more informed manner, and ultimately, enable us to reconstruct genes and species phylogenies more accurately. This thesis is an attempt to provide computational methods for phylogenetic inference and give tools to conduct genome-scale comparative evolutionary studies, such as detecting homologous sequences and inferring gene families. In the first project, we present FastPhylo as a software package containing fast tools for reconstructing distance-based phylogenies. It implements the previously published efficient algorithms for estimating a distance matrix from the input sequences and reconstructing an un-rooted Neighbour Joining tree from a given distance matrix. Results on simulated datasets reveal that FastPhylo can handles hundred of thousands of sequences in a minimum time and memory efficient manner. The easy to use, well-defined interfaces, and the modular structure of FastPhylo allows it to be used in very large Bioinformatic pipelines. In the second project, we present a synteny-aware gene homology method, called GenFamClust (GFC) that uses gene content and gene order conservation to detect homology. Results on simulated and biological datasets suggest that local synteny information combined with the sequence similarity improves the detection of homologs. In the third project, we introduce a novel phylogeny-based clustering method, PhyloGenClust, which partitions a very large gene family into smaller subfamilies. ROC (receiver operating characteristics) analysis on synthetic datasets show that PhyloGenClust identify subfamilies more accurately. PhyloGenClust can be used as a middle tier clustering method between raw clustering methods, such as sequence similarity methods, and more sophisticated Bayesian-based phylogeny methods. Finally, we introduce a novel probabilistic Bayesian method based on the DLTRS model, to sample reconciliations of a gene tree inside a species tree. The method uses MCMC framework to integrate LGTs, gene duplications, gene losses and sequence evolution under a relaxed molecular clock for substitution rates. The proposed sampling method estimates the posterior distribution of gene trees and provides the temporal information of LGT events over the lineages of a species tree. Analysis on simulated datasets reveal that our method performs well in identifying the true temporal estimates of LGT events. We applied our method to the genome-wide gene families for mollicutes and cyanobacteria, which gave an interesting insight into the potential LGTs highways.

QC 20161010

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Wilber, Matthew. "Building a History of Horizontal Gene Transfer in E. Coli". Scholarship @ Claremont, 2016. http://scholarship.claremont.edu/hmc_theses/75.

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Bacteria's ability to pass entire genes between one another, a process called Horizontal Gene Transfer (HGT), has a major impact on bacterial evolution. In an ongoing project at Harvey Mudd, computational methods have been used to catalogue the HGT events that have impacted a group of closely related bacteria. This thesis builds on that project, by improving our ability to identify gene families --- groups of genes in different strains that are related. Previously, similarity was measured only by comparing two genes' DNA sequences, ignoring their positions on the organism's DNA. Here, we leverage genes' relative position to make a better measurement of gene similarity. These improved similarity measurements will improve the existing pipeline's ability to identify HGT events.

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Yan, Yongpan. "Computational analyses of microbial genomes operons, protein families and lateral gene transfer /". College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/2596.

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Thesis (Ph. D.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

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Andam, Cheryl Marie Palacay. "Role of lateral gene transfer in the evolution of legume nodule symbionts". Diss., Online access via UMI:, 2007.

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Popa, Ovidiu-Nicolae [Verfasser]. "Directed phylogenomic networks of lateral gene transfer during prokaryotic evolution / Ovidiu-Nicolae Popa". Kiel : Universitätsbibliothek Kiel, 2016. http://d-nb.info/1094661988/34.

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Santos, Viviane Piccin dos [UNESP]. "Filogenia molecular de cianobactérias baseada em sequências do 16S-23S-ITS rDNA e PC-IGS: investigação de transferência lateral do PC". Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/87867.

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Made available in DSpace on 2014-06-11T19:23:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-17Bitstream added on 2014-06-13T19:28:52Z : No. of bitstreams: 1 santos_vp_me_rcla.pdf: 692384 bytes, checksum: 87577700198a680d7662c5fe0990efe7 (MD5)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
As cianobactérias apresentam uma ampla variabilidade fenotípica e ecológica. Porém, esta variabilidade, muitas vezes, não corresponde à sua diversidade genética. Assim, o uso de marcadores moleculares é fundamental para os estudos de filogenia neste grupo. Entretanto, a filogenia molecular enfrenta um desafio na seleção dos marcadores devido à ocorrência relativamente frequente da transferência de genes de forma lateral entre os procariotos. Em cianobactérias os marcadores dos espaçadores dos genes ribossomais (16S-23S-ITS rDNA) e do operon da ficocianina (PC-IGS) estão entre os mais utilizados nestes estudos. Contudo, alguns trabalhos sugerem que o PC-IGS possa ter sito transferido lateralmente em sua história evolutiva. A identificação de morfoespécies dos gêneros Microcystis e Geitlerinema é baseada em caracteres morfológicos que em geral não correspondem à sua variabilidade genética. Com o objetivo de investigar a transferência lateral do operon da ficocianina em Geitlerinema e Microcystis, foram obtidas e comparadas árvores filogenéticas de ambas espécies baseadas nos marcadores PC-IGS e 16S-23S-ITS rDNA. As topologias das árvores obtidas para ambos os marcadores foram muito semelhantes e indicaram que o PC-IGS é estável e indicado para os estudos de taxonomia e filogenia de linhagens de Geitlerinema e Microcystis. Assim, hipótese inicial de transferência lateral foi refutada. Algumas linhagens tiveram seu posicionamento divergente entre um marcador e outro, o que ressalta a importância do uso de mais de um marcador em estudos de filogenia. O marcador PC-IGS apresentou melhor desempenho que 16S-23S-ITS rDNA. As árvores filogenéticas de Geitlerinema baseadas em ambos os marcadores indicaram a ocorrência de espécies crípticas dentre as linhagens estudadas e corroboraram que G. amphibium e G. unigranulatum devem ser consideradas sinonímias...
Cyanobacteria show a wide phenotypic and ecological variability, but frequently this variability does not correspond to their genetic variation. Therefore, the use of molecular markes is critical for phylogenetic studies in this group. At the same time, the selection of molecular markers represents a challenge for the molecular phylogeny due to the horizontal gene transfer, witch is a relatively common process among the prokaryotes. In cyanobacteria, makers for the ribosomal genes spacer (16S-23S-ITS rDNA) and for the phycocyanin operon spacer (PC-IGS) are among of the most used for phylogeny. However, some studies suggest that the PC-IGS marker may have been horizontally transferred during its evolutionary history. The identification of the morphospecies from the genus Microcystis and Geitlerinema is based in their morphological characters, but they generally do not correspond to genetic variability. In order to investigate the possibility of horizontal transfer of the phycocyanin operon in Microcystis and Geitlerinema, phylogenetic trees based on the PC-IGS and 16S- 23S-ITS rDNA were generated and compared. The topologies obtained for both markers were very similar, indicating that the PC-IGS marker is stable and suitable for taxonomical and phylogenetic studies in Microcystis and Geitlerinema. Therefore, the initial hypothesis of horizontal transfer was rejected. Some strains were found to have divergent positions between the trees based on the two molecular markes, witch highlights the importance of using more than one marker in phylogenetic studies. The PC-IGS marker performed better than 16S-23SITS rDNA. The Geitlerinema phylogenetic trees based on both markers indicated the occurrence of cryptic species among the strains and corroborated that G. amphibium and G. unigranulatum should be treated as synonyms. The phylogenetic tree based on PC-IGS formed a monophyletic clade... (Complete abstract click electronic access below)

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Munoz, Víctor Hugo Anaya. "A theoretical model on the role of lateral gene transfer in the evolution of endosymbiotic genomes". Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16446.

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Laterale Gentransfer wurde zuerst von Schwartz und Dayhoff (1978) entdeckt, die es aber als eine Exzentrizität werteten und als solche ignorierten. Später, als mehrere DNS- und Eiweißsequenzen sequenziert und raffiniertere Phylogenien rekonstruiert wurden, hat die Rolle an Relevanz gewonnen, die der laterale (oder horizontale) Gentransfer in der evolutionären Geschichte von lebendigen Organismen gespielt hat. Außerdem existiert auch zwischen Endosymbionten und Zellkernen statt. Ich habe ein theoretisches Modell entwickelt, das den lateralen Gentransfer zwischen Endosymbionten und dem Zellkern repräsentiert. Das Modell erforscht die Bedeutung des Fehlens von Rekombination in den Organellen (Muller’s Ratchet) sowie Abweichungen von Muller’s Ratchet in Form der non-symmetrical homologous recombination in Gentransfermechanismen. Ich habe zum einen Zellkern-Inkompatibilitäten, die aus der Übertragung eines Gens resultieren, und zum anderen Zyto- und Zellkern-Inkompatibilitäten zwischen den mutierten endosymbiotischen Genomen und dem modifizierten Zellenkern untersucht. Die Ergebnisse zeigen, dass unter bestimmten Bedingungen die Existenz oder Nicht-Existenz von Rekombination die gleiche Wirkung haben können. Es zeigte sich auch, dass Rekombination, wenn sie vorkommt und wenn sie nicht symmetrisch ist, starke Auswirkungen auf die Allelenfrequenz einer Population haben kann. Es wurde auch klar, dass es eine starke Beziehung zwischen dem Zellkern und endosymbiotischen Genomen gibt, und dass das evolutionäre Schicksal des einen größtenteils von den evolutionären Kräften abhängig ist, die das andere beeinflussen. Wenn man Zellkern- und Cyto-Zellkerninkompatibilitäten in das Modell einführt, dann zeigen die Ergebnisse, dass die Inkompatibilitäten, die der laterale Gentransfer produziert hat, möglicherweise eine ähnliche Rolle im Speziationsmechanismus spielen könnten wie die Inkompatibilitäten zwischen Mitochondrien und Zellkernen in verschiedenen Nasonia-Arten.
Lateral gene transfer has played a key role in the evolution of living beings. This process was first acknowledged in 1978 by Schwartz and Dayhoff but considered a relatively infrequent eccentricity and ignored. Later on, as DNA and protein sequences accumulated and more refined phylogenies were reconstructed, the contribution of lateral (or horizontal) gene transfer to the evolutionary history of living organisms gained relevance. Besides, gene transfer is known to occur not only between independent organisms but also, and more frequently between endosymbionts including eukaryotic organelles. I developed a theoretical model to study the lateral gene transfer process between cell organelles (but extendible to other endosymbionts) and the cell nucleus. The model explores the role of the lack of recombination in the organelles (Muller''s ratchet) as well as deviations from Muller''s ratchet in the form of non-symmetrical homologous recombination in relation with the gene transfer process. Also, nuclear incompatibilities resulting from the inclusion of a transferred gene, and cyto-nuclear incompatibilities between the mutant endosymbiotic genomes and the modified nuclear genome are investigated. The results obtained show that under certain circumstances the existence recombination or its non-existence produce the same results, and that deviations from symmetry in the recombination process might have important effects on the frequency of different alleles. It is also clear that there is a strong relation between nuclear and endosymbiotic genomes, and that the evolutionary fate of one largely depends on the forces affecting the other. When nuclear and cyto-nuclear incompatibilities are introduced in the model, the results show that lateral gene transfer-induced incompatibilities could potentially play a role in the speciation process similar to the one produced by mitochondria in the Nasonia species.

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Kamali-Moghaddam, Masood. "Co-operative recombination mechanisms promoting gene clustering and lateral transfer of antibacterial drug resistance". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-4936-0/.

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Galindo, González Luis Javier. "Deep eukaryotic phylogenomics : the holomycota branch Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): an early Branching Microsporidium A new fungal clade helps reconstructing the tree of Fungi and the evolution of the flagellum in Holomycota Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage". Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS050.

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La plupart de la diversité biologique est en réalité microbienne. L'arbre phylogénétique des eucaryotes comprend plusieurs grands supergroupes monophylétiques, dont les Opisthokonta. Ce groupe comprend deux branches, les Holozoa, qui inclut les animaux, et les Holomycota, qui regroupe les champignons et leurs parents unicellulaires. Bien que les champignons multicellulaires soient bien connus, nos connaissances sur la diversité des champignons unicellulaires et de leurs parents phylogénétiques restent limitées. Cette fraction unicellulaire comprend plusieurs lignées zoosporiques (par exemple chytrids) au sein des champignons, mais aussi une variété de lignées liées aux champignons classiques : les nucleariids, les rozellids, les aphelids et les microsporidies. Cependant, les relations phylogénétiques de ces lignées entre elles et avec les champignons restent à établir solidement. Les arbres phylogénétiques des gènes d'ARNr 18S environnementaux montrent une grande diversité d'Holomycota unicellulaires dans la plupart des écosystèmes terrestres. Cependant, le signal phylogénétique de ce gène est limité et ne permet pas de résoudre la plupart des relations phylogénétiques profondes. Au cours des dernières années, les techniques à haut débit ont permis de séquencer des centaines de nouveaux génomes et transcriptomes. Cela a permis de réaliser des études phylogénomiques multi-gènes, qui augmentent le signal disponible pour résoudre les relations évolutives. Néanmoins, la plupart de ces génomes correspondent à des espèces fongiques faciles à cultiver, souvent avec un intérêt particulier pour l'homme. Actuellement, les approches de type « omique » à partir des cellules uniques se révèlent comme potentiellement utiles pour étudier les eucaryotes unicellulaires non cultivés, en permettant de reconstruire des analyses phylogénétiques robustes d'une grande diversité environnementale à l'aide de données génomiques et transcriptomiques. Au cours de mon travail de doctorat, j'ai appliqué des approches de « cellule unique » pour obtenir des informations phylogénétiques à partir de lignées Holomycota divergentes, clarifier les relations phylogénétiques entre les champignons et ses proches parents et inférer l'évolution de leurs traits. Plus précisément, j'ai utilisé cette approche pour :1) Générer des données génomiques et transcriptomiques pour les nucleariids et mieux reconstruire les relations internes dans le clade et les caractères présents dans leur ancêtre. Nos résultats confirment que les genres de protistes à thèque Pompholyxophrys et Lithocolla sont en effet des nucleariids et branchent avec Nuclearia, Parvularia et Fonticula. La reconstruction d'une phylogénie robuste de ce groupe nous a permis d’inférer les traits (par exemple pas de flagelle) ancestraux du groupe. 2) Séquencer et analyser de manière comparative le génome de Metchnikovella incurvata, pour confirmer sa position relativement basale dans Microsporidia et déterminer les synapomorphies du clade. L'analyse phylogénomique du metchnikovellid Metchnikovella incurvata a confirmé que des Metchnikovellidae branchent à la base des Core-Microsporidia. Nous avons également confirmé que leur profil métabolique était plus similaire à celui des Core-microsporidia, tous deux ayant réduit de manière similaire leurs gènes / fonctions. 3) Générer des données génomiques pour Amoeboradix gromovi et Sanchytrium tribonematis, qui forment le clade des sanchytrides, une nouvelle lignée de champignons zoosporiques identifiée récemment, et résoudre leur position phylogénétique. L'étude des deux génomes de sanchytrids a clarifié leur placement au sein des Fungi en tant que nouvelle groupe frère des Blastocladiomycota. Des analyses génomiques comparatives montrent que leur métabolisme est réduit par rapport aux lignées apparentées. En particulier, le système flagellaire est fortement réduit par rapport à d'autres Holomycota, avec 4 événements indépendants de perte de flagelle dans le clade
Despite the astonishing diversity of plants, animals and macroscopic fungi, most eukaryotic diversity is actually microbial. The eukaryotic tree comprises several large monophyletic supergroups. One of these groups is the Opisthokonta, which encompasses two branches, Holozoa, including animals, and Holomycota, grouping Fungi and their unicellular relatives. While multicellular fungi are well known, knowledge on the diversity of unicellular Fungi and their phylogenetic relatives is still poor. This unicellular fraction includes several zoosporic lineages (e.g. Chytridiomycota and Blastocladiomycota) within Fungi, but also a variety of lineages related to the classical core Fungi: nucleariids, rozellids, aphelids and Microsporidia. However, the phylogenetic relationships of these lineages among them and with classical Fungi remain to be solidly established. Molecular phylogenetic trees of 18S rRNA genes retrieved from environmental studies have showed a wide diversity of unicellular holomycotans in almost all environments on Earth. However, the phylogenetic signal of this gene is limited and does not allow robustly resolving most deep phylogenetic relationships. During past years, high-throughput techniques have allowed sequencing hundreds of new genomes and transcriptomes. This has made possible to carry out multi-gene phylogenomic studies, which increase the available signal to resolve evolutionary relationships. Nevertheless, most sequenced genomes correspond to easy-to-culture fungal species, often with particular interest for humans (e.g. parasites, plant symbionts, yeast). Recently, single-cell omics has become a potential useful approach to study uncultured unicellular eukaryotes, making it possible to reconstruct robust phylogenetic analyses of a wide environmental diversity using genomic and transcriptomic data. During my PhD work, I have applied single-cell techniques to get phylogenetic information from divergent holomycotan lineages, clarify phylogenetic relationships among fungi and their close relatives and infer trait evolution. More specifically, I have used this approach to: 1) Generate genomic and transcriptomic data for nucleariids and better reconstruct inner relationships in the clade and the characters present in the nucleariid ancestor. Our results confirm that the cover-bearing unicellular genera Pompholyxophrys and Lithocolla are indeed nucleariids and branch together with Nuclearia, Parvularia and Fonticula. The reconstruction of a robust phylogeny for the group allowed us to infer the traits (e.g. no flagellum, glycocalyx, no cover) already present in their ancestor. 2) Sequence and comparatively analyze the genome of Metchnikovella incurvata, to confirm its relatively basal position within Microsporidia, and determine synapomorphies for the clade. Phylogenomic analysis of the metchnikovellid Metchnikovella incurvata confirmed that Metchnikovellidae branch at the base of Core-Microsporidia. We also confirmed their metabolic profile to be more similar to Core-microsporidia, being both similarly reduced in genes/functions. 3) Generate genomic data for Amoeboradix gromovi and Sanchytrium tribonematis, which form the newly described zoosporic fungal clade of sanchytrids, and resolve their phylogenetic position. The study of the two sanchytrid genomes clarified their placement within Fungi as a new clade sister to Blastocladiomycota. Comparative genomics showed that their metabolic composition was reduced in comparison with related lineages. This reduction was especially important in their flagellar toolkit when compared with other Holomycota, confirming 4 independent flagellum loss events in the clade

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Santos, Viviane Piccin dos. "Filogenia molecular de cianobactérias baseada em sequências do 16S-23S-ITS rDNA e PC-IGS : investigação de transferência lateral do PC /". Rio Claro : [s.n.], 2011. http://hdl.handle.net/11449/87867.

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Orientador: Maria do Carmo Bittencourt de Oliveira
Banca: Luiz Henrique Zanini Branco
Banca: Mariana Cabral de Oliveira
Resumo: As cianobactérias apresentam uma ampla variabilidade fenotípica e ecológica. Porém, esta variabilidade, muitas vezes, não corresponde à sua diversidade genética. Assim, o uso de marcadores moleculares é fundamental para os estudos de filogenia neste grupo. Entretanto, a filogenia molecular enfrenta um desafio na seleção dos marcadores devido à ocorrência relativamente frequente da transferência de genes de forma lateral entre os procariotos. Em cianobactérias os marcadores dos espaçadores dos genes ribossomais (16S-23S-ITS rDNA) e do operon da ficocianina (PC-IGS) estão entre os mais utilizados nestes estudos. Contudo, alguns trabalhos sugerem que o PC-IGS possa ter sito transferido lateralmente em sua história evolutiva. A identificação de morfoespécies dos gêneros Microcystis e Geitlerinema é baseada em caracteres morfológicos que em geral não correspondem à sua variabilidade genética. Com o objetivo de investigar a transferência lateral do operon da ficocianina em Geitlerinema e Microcystis, foram obtidas e comparadas árvores filogenéticas de ambas espécies baseadas nos marcadores PC-IGS e 16S-23S-ITS rDNA. As topologias das árvores obtidas para ambos os marcadores foram muito semelhantes e indicaram que o PC-IGS é estável e indicado para os estudos de taxonomia e filogenia de linhagens de Geitlerinema e Microcystis. Assim, hipótese inicial de transferência lateral foi refutada. Algumas linhagens tiveram seu posicionamento divergente entre um marcador e outro, o que ressalta a importância do uso de mais de um marcador em estudos de filogenia. O marcador PC-IGS apresentou melhor desempenho que 16S-23S-ITS rDNA. As árvores filogenéticas de Geitlerinema baseadas em ambos os marcadores indicaram a ocorrência de espécies crípticas dentre as linhagens estudadas e corroboraram que G. amphibium e G. unigranulatum devem ser consideradas sinonímias... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Cyanobacteria show a wide phenotypic and ecological variability, but frequently this variability does not correspond to their genetic variation. Therefore, the use of molecular markes is critical for phylogenetic studies in this group. At the same time, the selection of molecular markers represents a challenge for the molecular phylogeny due to the horizontal gene transfer, witch is a relatively common process among the prokaryotes. In cyanobacteria, makers for the ribosomal genes spacer (16S-23S-ITS rDNA) and for the phycocyanin operon spacer (PC-IGS) are among of the most used for phylogeny. However, some studies suggest that the PC-IGS marker may have been horizontally transferred during its evolutionary history. The identification of the morphospecies from the genus Microcystis and Geitlerinema is based in their morphological characters, but they generally do not correspond to genetic variability. In order to investigate the possibility of horizontal transfer of the phycocyanin operon in Microcystis and Geitlerinema, phylogenetic trees based on the PC-IGS and 16S- 23S-ITS rDNA were generated and compared. The topologies obtained for both markers were very similar, indicating that the PC-IGS marker is stable and suitable for taxonomical and phylogenetic studies in Microcystis and Geitlerinema. Therefore, the initial hypothesis of horizontal transfer was rejected. Some strains were found to have divergent positions between the trees based on the two molecular markes, witch highlights the importance of using more than one marker in phylogenetic studies. The PC-IGS marker performed better than 16S-23SITS rDNA. The Geitlerinema phylogenetic trees based on both markers indicated the occurrence of cryptic species among the strains and corroborated that G. amphibium and G. unigranulatum should be treated as synonyms. The phylogenetic tree based on PC-IGS formed a monophyletic clade... (Complete abstract click electronic access below)
Mestre

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Oliveira, Amanda Carolina Paulino de [UNESP]. "Caracterização de transglicosilases líticas de mureína em xanthomonas citri subsp. citri 306 e estudo funcional das lts mltb2.1 e mltb2.2 associadas ao elemento Tnxax1". Universidade Estadual Paulista (UNESP), 2018. http://hdl.handle.net/11449/154759.

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Xanthomonas citri subsp. citri 306 (XccA) é o agente causal do cancro cítrico (CC), doença endêmica que afeta a citricultura. Durante a interação patógeno-hospedeiro o sistema de secreção tipo três (SST3) codificado pela XccA age na translocação de efetores e no estabelecimento da doença. A montagem do aparato de SST3 depende da síntese, remodelagem e degradação da parede celular bacteriana, sendo este processo realizado pela ação enzimática de transglicosilases líticas de mureína (LTs). XccA codifica diversas LTs, porém, pouco é conhecido sobre a diversidade de famílias e relação com a virulência. Dentre as LTs com provável relação com a virulência, duas ORFs parálogas presentes no cromossomo e plasmídeo pXAC64, respectivamente; são genes passageiros do TnXax1, um transposon da família Tn3, relacionado a evolução e emergência da patogenicidade nas Xanthomonadales. Portanto, este estudo objetivou elucidar o provável papel e diversidade das LTs presentes no genoma de XccA, caracterizando funcionalmente as LTs presentes em TnXax1 pela técnica de mutação sítio dirigida. Foram identificadas no genoma de XccA 13 LTs, sendo 12 pertencentes às famílias: 1A, 1B, 1C, 1D, 1F, 1G, 3A, 3B (2 cópias), 5A e 6A, e uma não classificada. A LT não classificada, é exclusiva do gênero Xanthomonas e relacionada à família 3B, porém contém um domínio adicional relacionado ao metabolismo de carboidratos. As LTs classificadas em famílias apresentam provável função relacionada com a remodelagem da parede celular para inserção de sistemas de secreção tipo 3, 4 e 6, inserção de flagelo, divisão celular, reciclagem da parede celular e degradação e controle da produção do peptidoglicano. As LTs do TnXax1 pertencem a família 3B, não são essenciais para XccA e desenvolvimento do CC, porém estão relacionadas ao aumento da virulência, diminuição da formação de biofilme, agregação e aumento na produção de goma xantana, corroborando o papel do TnXax1 como agente propagador da patogenicidade e virulência em Xanthomonadales. Em resumo, os resultados lançam novos conhecimentos frente ao papel das LTs com o metabolismo do peptidoglicano e relação com os mecanismos de transferência lateral, virulência e patogenicidade de XccA.
Xanthomonas citri subsp. citri 306 (XccA) is a causal agent of type A citrus canker (CC), one of the most devastating citriculture diseases. Type 3 Secretion Systems (T3SS) play a fundamental role in XccA pathogenicity. T3SS components are embedded in the bacterial inner and outer membrane and act as a channel for injection of effector proteins directly into the plant host cell cytosol. T3SS assembly and installation relies on bacterial cell wall synthesis, remodeling and degradation. Murein lytic transglycosylases (LT) are important in this process and are responsible for peptidoglycan cleavage and its remodeling. Information about the XccA LT arsenal is scarce: little is known about family diversity, their exact role and their connection to virulence in this bacterium. Among the LTs with probable relation to virulence, two paralogue ORFs (one in chromosome, one in pXAC64 plasmid) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role for evolution and emergence of pathogenicity in Xanthomonadales. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (2 copies), 1F, 1G, 3A, 3B (2 copies), 5A, 6A and one which is non-categorized. This noncategorized gene, is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism, whilst the other catalyzes peptidoglycan biosynthesis, and is widely distributed in gammaproteobacteria. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LTs (3B family) are not essential to XccA and CC development but are implicated in virulence, biofilm production and aggregation decrease and xanthan gum production increase, corroborating the role of TnXax1 transposon as a virulence and pathogenicity propagating agent in XccA. These findings also suggest that LTs acquisition by horizontal gene transfer mediated by TnXax1 improved bacterial fitness, bringing adaptive advantages to the plant-pathogen interaction process.
33004102070P6

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Driscoll, Timothy. "Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data". Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/50921.

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Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a genome sequence for the host. Metagenomic analysis typically avoid the host sequences in order to analyze community composition and functional diversity of the bacterial component. This dissertation describes the development of a novel approach at the intersection of genomics and metagenomics, aimed at the extraction and characterization of bacterial sequences from heterogeneous sequence data using phylogenomic and bioinformatic tools. To achieve this objective, three interoperable workflows were constructed as modular computational pipelines, with built-in checkpoints for periodic interpretation and refinement. The MetaMiner workflow uses 16S small subunit rDNA analysis to enable the systematic discovery and classification of bacteria associated with a host genome sequencing project. Using this information, the ReadMiner workflow comprehensively extracts, assembles, and characterizes sequences that belong to a target microbe. Finally, AssemblySifter examines the genes and scaffolds of the eukaryotic genome for sequences associated with the target microbe. The combined information from these three workflows is used to systemically characterize a bacterial target of interest, including robust estimation of its phylogeny, assessment of its signature profile, and determination of its relationship to the associated eukaryote. This dissertation presents the development of the described methodology and its application to three eukaryotic genome projects. In the first study, the genomic sequences of a single, known endosymbiont was extracted from the genome sequencing data of its host. In the second study, a highly divergent endosymbiont was characterized from the assembled genome of its host. In the third study, genome sequences from a novel bacterium were extracted from both the raw sequencing data and assembled genome of a eukaryote that contained significant amounts of sequence from multiple competing bacteria. Taken together, these results demonstrate the usefulness of the described approach in singularly disparate situations, and strongly argue for a sophisticated, multifaceted, supervised approach to the characterization of host-associated microbes and their interactions.
Ph. D.

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Albaaj, Mohammed. "Diversity of β-Lactamase Genes in Gram-Negative Soil Bacteria from Northwest Ohio". Bowling Green State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1566553116919146.

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Xie, Gang. "Evolution of aromatic metabolism a genomic perspective on the complexity contributed by genome expansion, reductive evolution, and lateral gene transfer /". [Gainesville, Fla.] : University of Florida, 2002. http://purl.fcla.edu/fcla/etd/UFE1001196.

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Arellano, Davin Adrian. "Utilisation des transferts horizontaux de gènes pour dater des phylogénies". Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1299.

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Le fait d'avoir une généalogie datée des organismes vivants est l'un des principaux objectifs de la biologie évolutive. Cette entreprise est confrontée à deux défis majeurs. Le premier est la rareté et l'incomplétude des enregistrements fossiles, pratiquement inexistants pour les microbes et essentiels pour fournir une échelle temporelle de l'histoire de la vie. Le second est la difficulté intrinsèque d'obtenir des phylogénies d'organismes dont le génome a été largement façonné par transfert latéral de gène (TLG). L'acquisition par transfert de nouveaux gènes d'origine éloignée perturbe des arbres de gènes et rend beaucoup plus complexe la reconstruction de l'histoire des espèces. Dans ce travail de thèse, je montre comment nous pouvons utiliser ces différences entre arbres de gènes et arbres d'espèces à notre avantage pour inférer les événements anciens de TLG et comment ils peuvent fournir une nouvelle échelle de temps pour l'évolution des organismes vivants. Les transferts étant particulièrement fréquents chez les espèces dont les fossiles sont rares, ils peuvent servir de nouvelle source de datation indépendante du registre géologique pour reconstruire une phylogénie datée de la vie. Dans la première partie, je réalise une analyse à l'échelle génomique pour montrer comment les méthodes de réconciliations phylogénétiques peuvent être utilisées pour détecter les lignées correspondant aux donneurs et aux receveurs des événements de TLG. En outre, ces méthodes fournissent également une vue détaillée de la façon dont les familles de gènes évoluent le long des arbres de l'espèce. En utilisant ALE, un logiciel de réconciliation probabiliste qui prend en compte l'incertitude dans les arbres de gènes, nous sommes en mesure de cartographier les événements de duplication, de perte et de transfert dans les phylogénies des cyanobactéries et des champignons. Nous montrons également comment les méthodes qui ignorent l'information contenue dans les arbres de gènes sous-estiment la fréquence réelle des TLG. Dans la deuxième partie, je présente en détail comment le TLG porte un signal temporel et comment ce signal peut être utilisé pour inférer des arbres datés. J'introduis une nouvelle méthode appelée MaxTiC qui permet de trouver un ordonnancement des noeuds dans l'arbre des espèces qui maximise la cohérence temporelle entre les transferts. Par des simulations, nous montrons la robustesse de la méthode aux erreurs présentes dans l'arbre des espèces et le nombre de familles de gènes nécessaires pour obtenir des arbres datés fiables. Enfin, pour confirmer nos résultats, je présente différentes approches permettant de comparer les temps de divergence découlant des transferts avec ceux estimés en utilisant des horloges moléculaires. Nous effectuons une analyse phylogénomique pour détecter des milliers d'événements de TLG dans quatres groupes: les cyanobactéries, les Deltaproteobactéries, les Archées et les Champignons. Nous trouvons un large accord entre les deux méthodes de datation, ce résultat étant robuste à l'utilisation de différentes prior sur les temps de divergence et différents modèles d'horloges moléculaires relâchées. Nous montrons également que certaines des dates indiquées par l'utilisation de TLG sont en désaccord avec les horloges moléculaires tout en étant soutenues par un grand nombre de TLG. Ces résultats suggèrent que l'utilisation des TLG pourrait permettre d'améliorer les méthodes de datation, notamment pour les phylogénies anciennes et ainsi conduire à d'importants changements de notre point de vue sur l'histoire de la vie
Having a dated genealogy of living organisms is one of the major goals of evolutionary biology. This enterprise faces two major challenges. The first one is the scarcity and incompleteness of the fossil record, virtually nonexistent for microbes and essential to provide a time scale of life history. The second one is the intrinsic difficulty of obtaining phylogenies in organisms whose genome has been extensively shaped by Lateral Gene Transfer (LGT). The acquisition of new genes from distant organisms creates important differences among genes trees and complicates the reconstruction of the species history. In this thesis work I show how we can use those differences to our advantage to infer ancient events of LGT and how they provide a temporal scale of evolution. Transfers can supply an important amount of information on divergence times in organisms whose fossils are very scarce, acting as a new dating source independent of the geological record and taking us a step closer to building a whole dated phylogeny of Life. In the first part, I perform genomic-scale analyses to show how phylogenetic reconciliations can be used to detect donor and recipient lineages of LGT events. Moreover, they also provide a detailed view of how gene families evolve along species trees. Using ALE, a probabilistic reconciliation software that accounts for the uncertainty in gene trees, we are able to map events of duplication, loss and transfer in phylogenies of cyanobacteria and fungi. We also show how methods that ignore the information contained in gene trees underestimate the real frequency of LGT. In the second part, I present in detail how LGT carries a temporal signal and how this signal can be used to infer dated trees. I explain a new method called MaxTiC, that finds the best dated tree by maximizing the number of transfers that are time-compatible with a phylogeny. By simulations we show how robust the method is to errors in the species tree and how many gene families are required to obtain reliable dated trees. Finally, to confirm our results I present different metrics to compare the divergence times inferred by transfers with those inferred by molecular clocks. We perform a phylogenomic analysis to detect thousands of LGT events in cyanobacteria, Deltaproteobacteria, Archaea and fungi and obtain their dated phylogenies. We find a broad agreement between both dating methods, a result robust to the use of different priors on divergence times and different models of relaxed molecular clock. We also show that some of the dates inferred by using LGT are not recovered by molecular clocks. These results altogether suggest that the use of LGT in future dating studies may have a big impact on the inferred dates of major evolutionary events and can lead to an important change of our view of the History of Life

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Jerlström-Hultqvist, Jon. "Hidden Diversity Revealed : Genomic, Transcriptomic and Functional Studies of Diplomonads". Doctoral thesis, Uppsala universitet, Mikrobiologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-182831.

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The diplomonads are a diverse group of eukaryotic microbes found in oxygen limited environments such as the intestine of animals were they may cause severe disease. Among them, the prominent human parasite Giardia intestinalis non-invasively colonizes the small intestine of humans and animals where it induces the gastrointestinal disease giardiasis. Two of the eight genetic groups of G. intestinalis, assemblage A and B, are known to infect humans and have zoonotic potential. At the start of project, genome scale data from assemblage B-H was either sparse or entirely missing. In this thesis, genome sequencing was performed on the assemblage B isolate GS (Paper I) and the P15 isolate (Paper III) of the hoofed-animals specific assemblage E to investigate the underlying components of phenotypic diversity in Giardia. Comparisons to assemblage A isolate WB revealed large genomic differences; entirely different repertoires of surface antigens, genome rearrangements and isolate specific coding sequences of potential bacterial origin. We established that genomic differences are also manifested at the transcriptome level (Paper VIII). In a follow up analysis (Paper IV) we concluded that the Giardia assemblages are largely reproductively isolated. The large genomic differences observed between Giardia isolates can explain the phenotypic diversity of giardiasis. The adaptation of diplomonads was further studied in Spironucleus barkhanus (Paper II), a fish commensal of grayling, that is closely related to the fish pathogen Spironucleus salmonicida, causative agent of systemic spironucleosis in salmonid fish. We identified substantial genomic differences in the form of divergent genome size, primary sequence divergence and evidence of allelic sequence heterozygosity, a feature not seen in S. salmonicida. We devised a transfection system for S. salmonicida (Paper VI) and applied it to the study of the mitochondrial remnant organelle (Paper VII). Our analyses showed that S. salmonicida harbor a hydrogenosome, an organelle with more metabolic capabilities than the mitosome of Giardia. Phylogenetic reconstructions of key hydrogenosomal enzymes showed an ancient origin, indicating a common origin to the hydrogenosome in parabasilids and diplomonads. In conclusion, the thesis has provided important insights into the adaptation of diplomonads in the present and the distant past, revealing hidden diversity.

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Avsaroglu, M. Dilek. "Isolation, Molecular Characterization Of Food-borne Drug Resistant Salmonella Spp. And Detection Of Class 1 Integrons". Phd thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/12608844/index.pdf.

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In this study, 59 epidemiologically unrelated Salmonella strains isolated from foods in Tü
rkiye and 49 Salmonella strains obtained from National Salmonella Reference Laboratories of Germany were analysed. For the characterization of strains, analyses such as serotyping, phage typing, antibiotyping and molecular biological characterization were done. The strains exhibited 17 different serotypes with S. Enteritidis serotype and PT21 phage type being the most prevalent in Turkish isolates. The highest antimicrobial resistance was observed against NAL for Turkish strains, whereas it was against SUL for strains from German origin. Molecular typing of all strains exhibited different plasmid profiles and PFGE patterns. There were 1-4 plasmids/profile for Turkish strains and 1-7 plasmids/profile for German strains. The PFGE patterns revealed 42 different subgroups, having two major clusters with 44,3% arbitrary homology. Among 72 resistant strains, the most prevalent resistance genotypes were observed as blatem-1 (%56, AMP resistance)
floR (%100, CHL and FFC resistance)
aphA1 (%100, KAN and NEO resistance)
tet(A) (%53, TET resistance)
aadA1 (%82, SPE and STR resistance)
sulI (%78, SUL resistance). The class I integron variable region analyses exhibited 700 bp (1 strain), 1000 bp (37 strain), 1200 bp (16 strain) and 1600 bp (3 strain) integrons.

24

Fonseca, Luciane Schons da. "Caracterization of the SOS response in Leptospira interrogans sorovar Copenhageni". Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-25032015-110306/.

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Leptospira is a basal genus in an ancient group of bacteria, the spirochetes. The pathogenic species are responsible for leptospirosis, a disease with worldwide distribution and of public health importance in developed tropical countries. L. interrogans serovar Copenhageni is the agent for the majority of human leptospirosis in Brazil. In this work, we used a great variety of experimental approaches to characterize the SOS system in this serovar, to identify its impact in general DNA damage response, as well as to assess the DNA repair toolbox owned by pathogenic and saprophytic leptospires. We identified an additional repressor LexA, acquired by lateral gene transfer, exclusively in serovar Copenhageni. We also observed that UV-C irradiation led to massive death of cells and blockage of cell division in the survivors. Both repressors were active and we identified the sequences responsible for binding to promoters. However, the LexA1 SOS box was redefined after a de novo motif search on LexA1 ChIP-seq enriched sequences. This regulator was able to bind to at least 25 loci in the genome. DNA damage also caused a massive rearrangement of metabolism: increase in expression was observed in transposon and prophage genes, in addition to DNA repair pathways and mutagenesis inducers; on the other hand, motility, general metabolism and almost all virulence genes were repressed. Two induced prophages provided several proteins with useful functions. We also assessed the DNA repair-related genes presented by the three species of Leptospira: the saprophytic L. biflexa, the facultative pathogen L. interrogans and the obligatory pathogen L. borgpetersenii. There are more diversity and redundancy of repair genes in L. interrogans in comparison with the other species. Lateral gene transfer seems to be an important supplier of DNA repair functions. In addition, leptospires share characteristics of both Gram-positives and Gram-negatives bacteria. Representative genes from several different pathways were induced during infection of susceptible mice kidneys, suggesting DNA repair genes are active while causing disease. All these data suggest mobile genetic elements are the major forces in leptospiral evolution. Moreover, during DNA damage response, several SOS-dependent and independent mechanisms are employed to decrease cell growth and virulence in favor of controlled induction of mechanisms involved in genetic variability.
Leptospira é um gênero basal em um grupo já considerado um dos mais ancestrais, as espiroquetas. As espécies patogênicas são responsáveis pela leptospirose, uma doença presente em todo o mundo e de principal importância em países tropicais em desenvolvimento. L. interrogans sorovar Copenhageni é o agente da maior parte dos casos no Brasil. Nesse trabalho, utilizamos diversas abordagens experimentais para caracterizar o sistema SOS nesse sorovar, identificar seu impacto na resposta geral a danos no DNA, assim como avaliar as funções de reparo de DNA disponíveis em leptospiras patogênicas e saprofíticas. Identificamos um repressor LexA adicional, adquirido por transferência horizontal e exclusivo do sorovar Copenhageni. Observamos também que irradiação por UV-C causou significativa morte celular e bloqueio da divisão celular dos sobreviventes. Ambos os repressores são ativos e identificamos as sequências que utilizam para se ligar aos promotores dos genes regulados. Entretanto, o SOS box de LexA1 foi redefinido após uma busca de novo por motivos enriquecidos nas sequências recuperadas por ChIP-seq. Esse regulador ligou-se ao menos a 25 locais do genoma. A maioria desses alvos teve aumento de expressão após UV-C. Danos no DNA também causaram um importante rearranjo metabólico: houve aumento de expressão em transposons e profagos, além de indutores de mutagênese e vias de reparo; por outro lado, mobilidade, crescimento celular e quase todos os fatores de virulência foram reprimidos. Dois profagos induzidos durante essa resposta, possivelmente proporcionam algumas proteínas de funções importantes. Nós também avaliamos a presença de genes envolvidos no reparo de DNA em três espécies de leptospira: L. biflexa, L. interrogans e L. borgpetersenii. L. interrogans é a espécie com maior diversidade e redundância de genes de reparo. Além disso, transferência horizontal parece ser um importante fornecedor de funções de reparo nesse gênero. Leptospiras também apresentam genes característicos tanto de bactérias Gram-positivas quanto Gram-negativas. Genes representando diferentes vias de reparo foram induzidos durante infecção em modelo animal, sugerindo que essas vias estão ativas no curso da doença. Todos esses dados, em conjunto, sugerem que elementos genéticos móveis são de extrema importância na evolução do gênero e das vias de reparo. Assim, durante a resposta a danos no DNA, diversos mecanismos dependentes e independentes de SOS são empregados para frear o crescimento celular e virulência em favor da indução controlada de mecanismos para aumentar variabilidade genética.

25

Anaya, Munoz Víctor Hugo Verfasser], Peter [Akademischer Betreuer] [Hammerstein, Hans-Jörg [Akademischer Betreuer] Rheinberger e Daniel Piñero [Akademischer Betreuer] Dalmau. "A theoretical model on the role of lateral gene transfer in the evolution of endosymbiotic genomes / Víctor Hugo Anaya Munoz. Gutachter: Peter Hammerstein ; Hans-Jörg Rheinberger ; Daniel Piñero Dalmau". Berlin : Humboldt Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://d-nb.info/1019165677/34.

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26

Petersen, Jörn. "Duplikationen und lateraler Transfer von Genen als Motor der Evolution : molekulare Studien am GAPDH-Gensystem von Grünalgen, Landpflanzen und Chlorarachniophyta /". [S.l. : s.n.], 1999. http://www.gbv.de/dms/bs/toc/307555755.pdf.

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27

Reboul, Guillaume. "Metabarcoding and metagenomic approaches to decipher microbial communities in suboxic environments Microbial eukaryotes in the suboxic chemosyn- thetic ecosystem of Movile Cave, Romania Hyper- diverse archaea near life limits at the polyextreme geothermal Dallol area Performance of the melting seawater-ice elution method on the metabarcoding characterization of benthic protist communities Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage Marine signature taxa and microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake". Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL041.

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L’écologie microbienne concerne l’étude des microorganismes et de leurs interactions biotiques et abiotiques dans un écosystème donné. Ces vingt dernières années, l’avancement des techniques moléculaires pour analyser la diversité microbienne et, notamment, les nouvelles technologies de séquençages (NGS) ont permis de surmonter les limitations associées aux approches traditionnelles basées sur la culture et la microscopie. Ces approches moléculaires ont conduit à une accumulation des données de diversité microbienne et de potentiel métabolique dans des communautés microbiennes des écosystèmes variés.Cependant, ces efforts ont été principalement appliqués sur des environnements facilement accessibles ou liés à l’humain, comme le plancton (marin principalement) et la flore intestinale. Néanmoins, ceci a conduit à une très forte augmentation de données environnementales et au développement de la bioinformatique par le biais de nombreux outils. Parmi les environnements délaissés des études, les environnements faibles en oxygène sont probablement également porteurs de nouveautés phylogénique ou métaboliques.Afin de palier à cela, nous avons choisi d’explorer deux environnements suboxiques relativement peu étudiés : la cave Movile (Roumanie) et les sédiments du lac Baikal (Sibérie, Russie). Notre but étant de montrer les diversités phylogénétiques et fonctionnelles des microbes de ces biotopes.Pour cela, j’ai d'abord développé un pipeline d’analyse de données métabarcoding (petite sous-unités ribosomique). Ensuite, j’ai appliqué cet outil sur des données de métabarcoding de protistes provenant d’échantillons d’eau et de tapis microbiens de la cave de Movile, un écosystème chemosynthétique pratiquement fermé. Nous avons montré que la diversité des protistes de la cave s’étendait à quasiment tous les grands groupes eucaryotes et provenait à la fois d’origine d’eaux douces et marines. De plus, la plupart ont été affiliées à des groupes d’organismes typiquement anaérobies, ce qui est concordant avec les paramètres abiotiques de la cave. Écologiquement, ces protistes sont des prédateurs mais aussi vraisemblablement des partenaires symbiotiques avec des espèces procaryotes de la cave.Dans une deuxième étude, j’ai eu l’opportunité d’appliquer ce pipeline de métabarcoding sur des données procaryotes et eucaryotes provenant des couches superficielles des sédiments du lac d’eau douce Baikal. Comme attendu, les communautés microbiennes dans ces sédiments sont particulièrement diverses et relativement enrichis en archées. Nous avons aussi pu mettre en évidence des lignées que l’on pensait exclusivement marines dans ces sédiments. Ces lignées sont probablement planctoniques mais s’accumulent au fond par sédimentation. Enfin, les échantillons ont été prélevés dans le but de tester les influences de la profondeur, du bassin et de la latitude sur les communautés. Aucune d’elles ne s’est révélée significative.Dans une troisième étude, j'ai utilisé une approche métagénomique afin de révéler les acteurs écologiquement majeurs dans les sédiments, leurs rôles et de reconstruire leurs génomes. Cela nous a permis notamment de mettre en évidence le rôle primordial des Thaumarchaeota dans le cycle de l’azote et la production primaire de molécules de carbone. Les chloroflexi et les protéobacteries ont aussi un rôle important dans la surface des sédiments du lac Baikal. Ce travail de thèse participe à la connaissance globale de la diversité microbienne sur la planète en mettant en lumière des environnements peu étudiés. De plus, l’étude de la surface des sédiments du lac Baikal apporte de nouvelles données sur le sujet de la transition eau douces/eau marines des microbes. Enfin, la métagénomique a permis de révéler le cycle des nutriments et les microorganismes y participant dans ces échantillons de sédiment. En résumé, ce travail vient mettre en lumière l’écologie microbienne d’écosystèmes suboxiques, notamment la surface des sédiments du lac Baikal
Microbial ecology is the science of micro-organisms and their biotic and abiotic interactions in a given ecosystem. As technology has advanced, molecular techniques have been widely used to overcome the limitations of classical approaches such as culturing and microscopy. Indeed, the development of Next Generation Sequencing (NGS) technologies in the past twenty years has largely helped to unravel the phylogenetic diversity and functional potential of microbial communities across ecosystems.Nonetheless, most of the environments studied through these techniques concentrated on relatively easily accessible, tractable and host-related ecosystems such as plankton (especially in marine ecosystems), soils and gut microbiomes. This has contributed to the rapid accumulation of a wealth of environmental diversity and metagenomic data along with advances in bioinformatics leading to the development of myriads of tools. Oxygen-depleted environments and especially their microbial eukaryote components are less studied and may lead to future phylogenetic and metabolic discoveries.In order to address this, we conducted analyses on two poorly studied suboxic ecosystems: Movile Cave (Romania) and lake Baikal sediments (Siberia, Russia). In this task, we aimed at unveiling the taxonomic and functional diversity of microorganims in these environments.To do so, I first evaluated the available bioinformatics tools and implemented a bioinformatics pipeline for 16S/18S rRNA gene-based metabarcoding analysis, making reasoned methodological choices. Then, as a case study, I carried out metabarcoding analyses of the water and floating microbial mats found in Movile Cave in order to investigate its protist diversity. Our study showed that Movile Cave, a sealed off chemosynthetic ecosystem, harbored a substantial protist diversity with species spanning most of the major eukaryotic super groups. The majority if these protists were related to species of freshwater and marine origins. Most of them were putatively anaerobic, in line with the cave environment, and suggesting that in addition to their predatory role, they might participate in prokaryote-protist symbioses.In a second study, I applied my metabarcoding pipeline to explore unique and relatively unexplored environment of Lake Baikal sediments. I first applied a metabarcoding approach using 16S and 18S rRNA genes to describe prokaryotic as well as protist diversity. Overall, the communities within these ecosystems were very diverse and enriched in ammonia-oxidizing Thaumarchaeota. We also identified several typical marine taxa which are likely planktonic but accumulate in sediments. Finally, our sampling plan allowed us to test whether differences across depth, basin or latitude affected microbial community structure. Our results showed that the composition of sediment microbial communities remained relatively stable across the samples regardless of depth or latitude.In a third study, we applied metagenomics to study the metabolic potential of communities associated to Baikal sediments and to reconstruct metagenome-assembled genomes (MAGs) of dominant organisms. This revealed the considerable ecological importance of Thaumarchaeota lineages in lake Baikal sediments, which were found to be the major autotrophic phyla and also very implicated in the nitrogen cycle. Chloroflexi and Proteobacteria-related species also appeared ecologically important.This PhD thesis reveals the taxonomic diversity of poorly studied suboxic ecosystems and therefore contributes to our knowledge of microbial diversity on Earth. Additionally, the analyses of surface sediment samples in lake Baikal adds new light on freshwater-marine transitions. The metagenomic analyses reported here allowed us to postulate a model of nutrient cycle carried out by microorganismsin these sediments. Overall, this work sheds light on the microbial ecology of oxygen-depleted environments, and most notably lake Baikal surface sediments

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Johansson, Carolina. "Mechanisms and DNA Specificity in Site-specific Recombination of Integron Cassettes". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7429.

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de, Koning Audrey Patricia. "Lateral gene transfer from bacteria to protists". Thesis, 2002. http://hdl.handle.net/2429/12456.

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The advent of genome-level sequencing has brought a wealth of genetic information that can be used to trace the evolution of organisms. Phylogenies based on homologous proteins often do not agree on implied species relationships, indicating that the evolutionary path taken by some of these genes differs from the evolution of the organisms. One explanation for this observed pattern is lateral gene transfer, the movement of genes across species boundaries. There are mechanisms to facilitate such movement in prokaryotic organisms. In eukaryotes, it is less clear what mechanisms might facilitate incorporation of foreign genes into a species' genome. Multicellular eukaryotes are presumably more resistant to lateral gene transfer, because the majority of their cells do not have access to genes from other organisms. Moreover, germ and somatic cell lineages are often separate, which greatly reduces the probability that any gene that gains access to a foreign cell will be heritable and subsequently become part of its host species' genome. Phagotrophic protists, however, represent one type of eukaryote where these restrictions do not exist. Such organisms commonly ingest bacteria as food, and chance events may lead to the incorporation and use of bacterial genes. Lateral gene transfer from organelles of symbiotic origin (the chloroplast and mitochondrion) to the nucleus of the host organism represents a specialized case of lateral gene transfer resulting from phagotrophy. Lateral gene transfer in eukaryotes, therefore, is expected to involve bacterial genes incorporated into the genomes of phagocytic species (or those that have evolved from them). Accordingly, genes of bacterial origin were sought among the genetic information available from protists. Over 2000 predicted genes from the genome-sequencing project for the malarial parasite, Plasmodium falciparum, were screened to find those that are highly similar to genes from bacterial species. Phylogenetic reconstruction methods were used to elucidate the evolution of 'bacteria-like' genes. Thirteen laterally transferred genes were identified on the basis of protein phylogeny, of which nine are probably transferred from symbiotic organelles and three appear to involve transfers with bacteria. The conclusion is that genes introduced to the genome through lateral gene transfer are not nearly as prevalent in this eukaryote as they are in bacteria.

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Eveleigh, Robert. "Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past". Thesis, 2011. http://hdl.handle.net/10222/14412.

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Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Here I outline these scenarios and consider the fit of the available data, including two recently sequenced genomes from members of the Aquificae, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the ?-Proteobacteria have the strongest affinities with the three Aquificae analyzed. However, this phylogenetic signal is by no means the dominant one, with the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class ?-Proteobacteria also showing strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: as observed previously, most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, while a wide range of metabolic systems strongly supported the Aquificae - ?-Proteobacteria link. Given the breadth of support for this latter relationship, a scenario of ?-proteobacterial ancestry coupled with frequent exchange among thermophilic lineages is a plausible explanation for the emergence of the Aquificae.

31

Mukhopadhyay, Aindrila. "Initiating lateral gene transfer : analysis of the VirA/VirG two component system in vivo /". 2002. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3070198.

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Meehan, Conor J., e R. G. Beiko. "A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria". 2014. http://hdl.handle.net/10454/17256.

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Yes
Several bacterial families are known to be highly abundant within the human microbiome, but their ecological roles and evolutionary histories have yet to be investigated in depth. One such family, Lachnospiraceae (phylum Firmicutes, class Clostridia) is abundant in the digestive tracts of many mammals and relatively rare elsewhere. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of many species within the group with the production of butyric acid, a substance that is important for both microbial and host epithelial cell growth. We examined the genomes of 30 Lachnospiraceae isolates to better understand the origin of butyric acid capabilities and other ecological adaptations within this group. Butyric acid production-related genes were detected in fewer than half of the examined genomes with the distribution of this function likely arising in part from lateral gene transfer (LGT). An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possess genes for endospore formation, whereas other members of this family lack key sporulation-associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity, and bovine rumen. Our analysis demonstrates that adaptation to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and LGT.
Canadian Institute for Health Research (grant number CMF-108026), Genome Atlantic and the Canada Research Chairs program to R.G.B.

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Hall, Charles Robert. "The Contribution of Horizontal Gene Transfer to the Evolution of Fungi". Diss., 2007. http://dukespace.lib.duke.edu/dspace/bitstream/10161/202/1/D_Hall_Charles_Robert_a_052007.pdf.

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Whidden, Chris. "Efficient Computation and Application of Maximum Agreement Forests". 2013. http://hdl.handle.net/10222/35349.

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Rampant lateral gene transfer (LGT) among prokaryotes, hybridization in plants and other reticulate evolutionary processes invalidate typical phylogenetic tree models by violating the assumption that organisms only inherit genetic information from a single parent species. Comparing the different evolutionary histories of multiple genes is necessary to identify and assess these processes. In this work I develop efficient approximation and fixed-parameter algorithms for computing rooted maximum agreement forests (MAFs) and maximum acyclic agreement forests (MAAFs) of pairs of phylogenetic trees. Their sizes correspond to the subtree-prune-and-regraft (SPR) distance and the hybridization number of these pairs of trees, which are important measures of the dissimilarity of phylogenies used in studying reticulate evolution. Although these MAFs and MAAFs are NP-hard to compute, my fixed-parameter algorithms are practical because they scale exponentially with the computed distance rather than the size of the trees. I contribute efficient fixed-parameter algorithms for computing MAFs and MAAFs of two binary rooted trees and give the first efficient fixed-parameter and approximation algorithms for computing MAFs of two multifurcating rooted trees. My open-source implementation of the MAF algorithms is orders of magnitude faster than previous approaches, reducing the time required to compute SPR distances of 46 between trees of 144 species to fractions of a second whereas previous approaches required hours to compute SPR distances of 25. These fast MAF-based distance metrics enable the construction of supertrees to reconcile a collection of gene trees and rapid inference of LGT. Simulations demonstrate that supertrees minimizing the SPR distance are more accurate than other supertree methods under plausible rates of LGT. I constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees covering 244 genomes from several major bacterial phyla and inferred "highways" of gene transfer between these bacterial classes and genera; a small number of these highways connect distantly related genera and can highlight specific genes implicated in long-distance LGT. These fast MAF algorithms are thus practical and enable new analyses of reticulate evolution.

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Rohrbacher, Fanny. "Structure fonctionnelle du plasmidome rhizosphérique dans un contexte de contamination aux hydrocarbures". Thèse, 2017. http://hdl.handle.net/1866/19565.

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La phytoremédiation, la technique de bioremédiation qui utilise les plantes, est considérée comme une technologie « verte » et efficace pour décontaminer des sols pollués aux hydrocarbures. Les plantes agissent essentiellement à travers la stimulation des microorganismes de la rhizosphère, où l’exsudation racinaire semble être le moteur majeur de l’activité microbienne qui s’y déroule. Beaucoup de gènes responsables de l’adaptation bactérienne, dans le sol contaminé ou dans la rhizosphère, semblent être portés par les plasmides conjugatifs et transférés entre les bactéries. Une meilleure compréhension de ce phénomène pourrait améliorer le développement de techniques de manipulation du microbiome rhizosphérique afin d’accélérer la bioremédiation. Le but de cette recherche est d’étudier le plasmidome, soit le contenu total en plasmides, de la rhizosphère de saules provenant d’un sol contaminé aux hydrocarbures. Des analyses métagénomiques, de données obtenues à partir d’un séquençage Illumina, ont été utilisées pour étudier les fonctions portées par les plasmides. Nos résultats ont indiqué un fort effet de la contamination aux hydrocarbures sur la composition des plasmides. De plus, les plasmides contenaient des gènes impliqués dans de nombreuses voies métaboliques, telles que la biodégradation d’hydrocarbures, la production d’énergie, la transduction du signal, le chimiotactisme, et les métabolismes des sucres, acides aminés et métabolites secondaires. À ce jour, c’est la première étude de métagénomique comparative documentant la diversité des plasmides dans un contexte de phytoremédiation. Ces résultats fournissent de nouvelles connaissances sur le rôle du transfert latéral de gènes dans l’adaptation bactérienne dans la rhizosphère et dans le sol contaminé aux hydrocarbures.
Phytoremediation, a bioremediation technique that uses plants, is considered to be an effective and affordable “green technology” to clean up hydrocarbon contaminated soils. Plants essentially act indirectly through the stimulation of rhizosphere microorganisms. Root exudation is thought to be one of the predominant drivers of microbial communities in the rhizosphere and is therefore a potential key factor behind enhanced hydrocarbon biodegradation. Many of the genes responsible for bacterial adaptation in contaminated soil and the plant rhizosphere are thought to be carried by conjugative plasmids and transferred among bacteria. A better understanding of these phenomena could thus inform the development of techniques to manipulate the rhizospheric microbiome in ways that improve hydrocarbon bioremediation. This research aims to study the plasmidome (the overall plasmid content) in the rhizosphere of willow growing in hydrocarbon contaminated and non-contaminated soils, as compared with unplanted soil. Metagenomic analyses based on Illumina sequencing were used to highlight functions carried by plasmids. Our results indicate a strong effect of hydrocarbon contamination on plasmid composition. Furthermore, plasmids harbored genes involved in several metabolic pathways, such as hydrocarbon biodegradation, energy production, signal transduction, chemotaxis, metabolisms of carbohydrates, amino acids and secondary metabolites. To date, this is the first comparative soil metagenomics documenting the plasmidome diversity in a phytoremediation system. The results provide new knowledge on the role of lateral gene transfer in the bacterial adaptation in rhizosphere and in hydrocarbon contaminated soil.

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Petersen, Jörn [Verfasser]. "Duplikationen und lateraler Transfer von Genen als Motor der Evolution: Molekulare Studien am GAPDH-Gensystem von Grünalgen, Landpflanzen und Chlorarachniophyta / von Jörn Petersen". 1999. http://d-nb.info/958119082/34.

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